SimPheny ID abbreviation new since iJR904 officialName formula charge casNumber KEGG cmpd ID notes 286 10fthf No 10-Formyltetrahydrofolate C20H21N7O7 -2 692-29-5 C00234 "KEGG - C00234 Neutral MF = C20H23N7O7 SMP CHS checked N groups - NCD Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR" 26140 12dgr120 Yes "1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0)" C27H52O5 0 C00641 KEGG - C00641 AMF 26106 12dgr140 Yes "1,2-Diacyl-sn-glycerol (ditetradecanoyl, n-C14:0)" C31H60O5 0 C00641 KEGG - C00641 AMF 26115 12dgr141 Yes "1,2-Diacyl-sn-glycerol (ditetradec-7-enoyl, n-C14:1)" C31H56O5 0 C00641 KEGG - C00641 AMF 26113 12dgr160 Yes "1,2-Diacyl-sn-glycerol (dihexadecanoyl, n-C16:0)" C35H68O5 0 C00641 KEGG - C00641 AMF 26116 12dgr161 Yes "1,2-Diacyl-sn-glycerol (dihexadec-9-enoyl, n-C16:1)" C35H64O5 0 C00641 KEGG - C00641 AMF 26114 12dgr180 Yes "1,2-Diacyl-sn-glycerol (dioctadecanoyl, n-C18:0)" C39H76O5 0 C00641 KEGG - C00641 AMF 26117 12dgr181 Yes "1,2-Diacyl-sn-glycerol (dioctadec-11-enoyl, n-C18:1)" C39H72O5 0 C00641 KEGG - C00641 AMF 2181 12ppd-R Yes "(R)-Propane-1,2-diol" C3H8O2 0 4254-14-2 C02912 KEGG - C02912 SMP CHS 1889 12ppd-S No "(S)-Propane-1,2-diol" C3H8O2 0 4254-14-2 C02917 KEGG - C02917 SMP CHS 288 13dpg No 3-Phospho-D-glyceroyl phosphate C3H4O10P2 -4 None C00236 KEGG - C00236 Neutral MF = C3H8O10P2 SMP CHS 22230 14glucan Yes "1,4-alpha-D-glucan" C36H62O31 0 "AMF made up formula to match malthx, the highest carbon maltodextrin that is transported in the model" 1359 15dap No "1,5-Diaminopentane" C5H16N2 2 462-94-2 C01672 KEGG - C01672 Neutral Compound SMP CHS Changed according to Genomatica JLR 26390 1agpe120 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) C17H36NO7P1 0 C04438 KEGG - C04438 AMF 26391 1agpe140 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) C19H40NO7P1 0 C04438 KEGG - C04438 AMF 26392 1agpe141 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) C19H38NO7P1 0 C04438 KEGG - C04438 AMF 26393 1agpe160 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) C21H44NO7P1 0 C04438 KEGG - C04438 AMF 26394 1agpe161 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) C21H42NO7P1 0 C04438 KEGG - C04438 AMF 26395 1agpe180 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) C23H48NO7P1 0 C04438 KEGG - C04438 AMF 26396 1agpe181 Yes 1-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) C23H46NO7P1 0 C04438 KEGG - C04438 AMF 26383 1agpg120 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) C18H36O9P1 -1 AMF 26384 1agpg140 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) C20H40O9P1 -1 AMF 26385 1agpg141 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) C20H38O9P1 -1 AMF 26386 1agpg160 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) C22H44O9P1 -1 AMF 26387 1agpg161 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) C22H42O9P1 -1 AMF 26388 1agpg180 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) C24H48O9P1 -1 AMF 26389 1agpg181 Yes 1-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) C24H46O9P1 -1 AMF 26132 1ddecg3p Yes 1-dodecanoyl-sn-glycerol 3-phosphate C15H29O7P1 -2 C00681 KEGG - C00681 AMF 26054 1hdec9eg3p Yes 1-hexadec-9-enoyl-sn-glycerol 3-phosphate C19H35O7P1 -2 AMF 26051 1hdecg3p Yes 1-hexadecanoyl-sn-glycerol 3-phosphate C19H37O7P1 -2 C00681 AMF 26055 1odec11eg3p Yes 1-octadec-11-enoyl-sn-glycerol 3-phosphate C21H39O7P1 -2 AMF 26052 1odecg3p Yes 1-octadecanoyl-sn-glycerol 3-phosphate C21H41O7P1 -2 C00681 AMF 2994 1pyr5c No 1-Pyrroline-5-carboxylate C5H6NO2 -1 C03912 "KEGG - C03912 Neutral MF = C5H7NO2 SMP CHS Checked N-groups JLR,NCD" 26053 1tdec7eg3p Yes 1-tetradec-7-enoyl-sn-glycerol 3-phosphate C17H31O7P1 -2 C00681 AMF 26050 1tdecg3p Yes 1-tetradecanoyl-sn-glycerol 3-phosphate C17H33O7P1 -2 C00681 AMF 1697 23camp Yes "2',3'-Cyclic AMP" C10H11N5O6P -1 9014-63-5 C02353 KEGG - C02353 AMF 1698 23ccmp Yes "2',3'-Cyclic CMP" C9H11N3O7P -1 C02354 KEGG - C02354 AMF 4602 23cgmp Yes "2',3'-Cyclic GMP" C10H11N5O7P -1 C06194 KEGG - C06194 AMF 1699 23cump Yes "2',3'-Cyclic UMP" C9H10N2O8P -1 9014-63-5 C02355 KEGG - C02355 AMF 18003 23dappa Yes "2,3-diaminopropionate" C3H9N2O2 1 C06393 MKA L- and D- forms not distinguished here 10362 23ddhb No "2,3-Dihydro-2,3-dihydroxybenzoate" C7H7O4 -1 C04171 KEGG - C04171 Neutral MF = C7H8O4 SMP CHS 258 23dhb No "2,3-Dihydroxybenzoate" C7H5O4 -1 303-38-8 C00196 KEGG - C00196 Neutral MF = C7H6O4 SMP CHS 15091 23dhba No "(2,3-Dihydroxybenzoyl)adenylate" C17H17N5O10P -1 C04030 "KEGG - C04030 Neutral MF = C17H18N5O10P SMP CHS Check groups AMF, JLR, SAB" 21297 23dhbzs Yes "2,3-dihydroxybenzoylserine" C10H10NO6 -1 AMF 2398 23dhdp No "2,3-Dihydrodipicolinate" C7H5NO4 -2 C03340 KEGG - C03340 Neutral MF = C7H7NO4 SMP CHS (close compound-dipicolinic acid has a pKa of 2.16 and 4.76) Checked N-groups JLR 3067 23dhmb No "(R)-2,3-Dihydroxy-3-methylbutanoate" C5H9O4 -1 C04272 KEGG - C04272 (C04039 Deleted) Neutral MF = C5H10O4 SMP CHS 3129 23dhmp No "(R)-2,3-Dihydroxy-3-methylpentanoate" C6H11O4 -1 C06007 KEGG - C06007 (C04104 Deleted) Neutral MF = C6H12O4 SMP CHS 4195 23doguln No "2,3-Dioxo-L-gulonate" C6H7O7 -1 583-08-4 C05409 KEGG - C05409 Neutral-C6H8O7 JLR 3554 25aics No (S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate C13H15N4O12P -4 C04823 KEGG - C04823 Neutral MF = C13H19N4O12P SMP CHS Checked N-groups JLR 9067 25dkglcn No "2,5-diketo-D-gluconate" C6H7O7 -1 C02780 KEGG C02780 Neutal - C6H8O7 JLR 8249 25drapp No "2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate" C9H14N5O8P -2 "Neidhardt, pg 658 JLR- similar to 25dhpp except ketone group in the nitrogen ring rather than the OH group Checked N-groups, agrees with ACD software, JLR" 11429 26dap-LL No "LL-2,6-Diaminoheptanedioate" C7H14N2O4 0 583-93-7 C00666 KEGG - C00666 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR 449 26dap-M No "meso-2,6-Diaminoheptanedioate" C7H14N2O4 0 None C00680 KEGG - C00680 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR 26342 2agpe120 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) C17H36NO7P1 0 C05973 KEGG - C05973 AMF 26345 2agpe140 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) C19H40NO7P1 0 C05973 KEGG - C05973 AMF 26346 2agpe141 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) C19H38NO7P1 0 C05973 KEGG - C05973 AMF 26344 2agpe160 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) C21H44NO7P1 0 C05973 KEGG - C05973 AMF 26347 2agpe161 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) C21H42NO7P1 0 C05973 KEGG - C05973 AMF 26343 2agpe180 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) C23H48NO7P1 0 C05973 KEGG - C05973 AMF 26348 2agpe181 Yes 2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) C23H46NO7P1 0 C05973 KEGG - C05973 AMF 26349 2agpg120 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) C18H36O9P1 -1 AMF 26351 2agpg140 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) C20H40O9P1 -1 AMF 26354 2agpg141 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) C20H38O9P1 -1 AMF 26352 2agpg160 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) C22H44O9P1 -1 AMF 26355 2agpg161 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) C22H42O9P1 -1 AMF 26353 2agpg180 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) C24H48O9P1 -1 AMF 26356 2agpg181 Yes 2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) C24H46O9P1 -1 AMF 437 2ahbut No (S)-2-Aceto-2-hydroxybutanoate C6H9O4 -1 C06006 KEGG - C06006 (C00659 Deleted) Neutral MF = C6H10O4 SMP CHS 21347 2amsa Yes 2-Aminomalonate semialdehyde C3H5NO3 0 C11822 0 2707 2aobut No L-2-Amino-3-oxobutanoate C4H7NO3 0 C03508 KEGG - C03508 (C03214 Deleted) Neutral MF = C4H7NO3 SMP CHS Checked N-groups JLR 7152 2cpr5p No 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate C12H13NO9P -3 C01302 KEGG - C01302 Neutral MF = C12H16NO9P SMP Checked N-groups JLR 3353 2dda7p No 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate C7H10O10P -3 C04691 KEGG - C04691 Neutral MF = C7H13O10P SMP CHS 26357 2ddecg3p Yes 2-dodecanoyl-sn-glycerol 3-phosphate C15H29O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 3930 2ddg6p No 2-Dehydro-3-deoxy-D-gluconate 6-phosphate C6H8O9P -3 C04442 KEGG - C04442 Neutral MF = C6H11O9P SMP CHS 264 2ddglcn No 2-Dehydro-3-deoxy-D-gluconate C6H9O6 -1 None C00204 KEGG - C00204 Neutral MF = C6H10O6 SMP CHS 946 2dh3dgal No 2-Dehydro-3-deoxy-D-galactonate C6H9O6 -1 C01216 KEGG - C01216 Neutral-C6H10O6 JLR 997 2dh3dgal6p No 2-Dehydro-3-deoxy-D-galactonate 6-phosphate C6H8O9P -3 C01286 KEGG - C01286 Neutral-C6H11O9P JLR 1118 2dhglcn No 2-Dehydro-D-gluconate C6H9O7 -1 C00629 KEGG - C00629 Neutral-C6H10O7 JLR 9068 2dhguln No 2-Dehydro-L-gulonate C6H9O7 -1 No Kegg entry Neutral- C6H10O7 JLR 800 2dhp No 2-Dehydropantoate C6H9O4 -1 C00966 KEGG - C00966 Neutral MF = C6H10O4 SMP CHS 4305 2dmmq8 No 2-Demethylmenaquinone 8 C50H70O2 0 C05818 KEGG - C05818 General Formula = C15H14O2(C5H8)n; n = 7 for 2dmmq8 SMP 6326 2dmmql8 No 2-Demethylmenaquinol 8 C50H72O2 0 JLR 446 2dr1p No 2-Deoxy-D-ribose 1-phosphate C5H9O7P -2 C00672 KEGG - C00672 Neutral MF = C5H11O7P SMP CHS 447 2dr5p No 2-Deoxy-D-ribose 5-phosphate C5H9O7P -2 102916-66-5 C00673 KEGG - C00673 Neutral MF = C5H11O7P SMP CHS 906 2h3oppan No 2-Hydroxy-3-oxopropanoate C3H3O4 -1 C01146 KEGG - C01146 Neutral-C3H4O4 JLR 26362 2hdec9eg3p Yes 2-hexadec-9-enoyl-sn-glycerol 3-phosphate C19H35O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 26359 2hdecg3p Yes 2-hexadecanoyl-sn-glycerol 3-phosphate C19H37O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 1886 2ippm No 2-Isopropylmaleate C7H8O4 -2 C02631 KEGG - C02631 Neutral MF = C7H10O4 SMP 5757 2kmb No 2-keto-4-methylthiobutyrate C5H7O3S -1 No KEGG Entry JEM has it as KMB Neutral MF = C5H8O3S SMP 3501 2mahmp No 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate C6H8N3O7P2 -3 745-65-3 C04752 KEGG - C04752 Neutral MF = C6H11N3O7P2 SMP Checked N-groups JLR 3219 2mcacn No cis-2-Methylaconitate C7H5O6 -3 99-98-9 C04225 KEGG - C04225 Neutral-C7H8O6 JLR 1591 2mcit No 2-Methylcitrate C7H7O7 -3 96-17-3 C02225 KEGG - C02225 NCD JLR 6321 2me4p No 2-C-methyl-D-erythritol 4-phosphate C5H11O7P -2 C11434 KEGG C11434 Neutral MF = C5H13O7P SMP 6331 2mecdp No "2-C-methyl-D-erythritol 2,4-cyclodiphosphate" C5H10O9P2 -2 C11453 KEGG ID- C11453 Neutral MF = C5H12O9P2 SMP 1071 2obut No 2-Oxobutanoate C4H5O3 -1 600-18-0 C00109 KEGG - C00109 Neutral MF = C4H6O3 SMP CHS NCD 26363 2odec11eg3p Yes 2-octadec-11-enoyl-sn-glycerol 3-phosphate C21H39O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 26360 2odecg3p Yes 2-octadecanoyl-sn-glycerol 3-phosphate C21H41O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 10904 2ohph No 2-Octaprenyl-6-hydroxyphenol C46H70O2 0 C05811 KEGG - C05811 SMP CHS 8204 2ombzl No "2-Octaprenyl-6-methoxy-1,4-benzoquinol" C47H72O3 0 Neidhardt page 651 JLR 8212 2omhmbl No "2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol" C48H74O4 0 Neidhardt page 651 JLR 8207 2ommbl No "2-Octaprenyl-3-methyl-6-methoxy- 1,4-benzoquinol" C48H74O3 0 Neidhardt page 651 JLR 4483 2omph No 2-Octaprenyl-6-methoxyphenol C47H72O2 0 C05812 KEGG - C05812 SMP CHS 4482 2oph No 2-Octaprenylphenol C46H70O 0 C05810 KEGG - C05810 SMP CHS 11026 2p4c2me No 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H22N3O17P3 -4 No KEGG Entry Neutral MF = C14H26N3O17P3 SMP Checked N-groups JLR 1120 2pg No D-Glycerate 2-phosphate C3H4O7P -3 C00631 KEGG - C00631 Neutral MF = C3H7O7P SMP CHS 813 2pglyc No 2-Phosphoglycolate C2H2O6P -3 C00988 KEGG - C00988 Neutral MF = C2H5O6P SMP CHS 4304 2shchc No "2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate" C11H10O6 -2 C05817 KEGG - C05817 Neutral MF = C11H12O6 SMP CHS 26361 2tdec7eg3p Yes 2-tetradec-7-enoyl-sn-glycerol 3-phosphate C17H31O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 26358 2tdecg3p Yes 2-tetradecanoyl-sn-glycerol 3-phosphate C17H33O7P1 -2 52-52-8 C03974 KEGG - C03974 AMF 21298 2tpr3dpcoa Yes 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA C26H40N7O26P5S -6 AMF 3087 34dhpac Yes "3,4-Dihydroxyphenylacetaldehyde" C8H8O3 0 145-14-2 C04043 KEGG - C04043 SAB 772 34hpp No 3-(4-Hydroxyphenyl)pyruvate C9H7O4 -1 C01179 KEGG - C01179 Neutral MF = C9H8O4 SMP CHS 18604 3amp Yes 3'-AMP C10H12N5O7P -2 84-21-9 C01367 MKA AMF 2681 3c2hmp No 3-Carboxy-2-hydroxy-4-methylpentanoate C7H10O5 -2 C04411 KEGG - C04411 Neutral MF = C7H12O5 SMP CHS 1803 3c3hmp No 3-Carboxy-3-hydroxy-4-methylpentanoate C7H10O5 -2 C02504 KEGG - C02504 Neutral MF = C7H12O5 SMP CHS 3228 3c4mop No 3-Carboxy-4-methyl-2-oxopentanoate C7H8O5 -2 C04236 KEGG - C04236 Neutral MF = C7H10O5 SMP 18607 3cmp Yes 3'-cmp C9H12N3O8P -2 C05822 MKA AMF 1111 3dhguln No 3-Dehydro-L-gulonate C6H9O7 -1 C00618 KEGG - C00618 Neutral-C6H10O7 JLR NCD MKA 9125 3dhgulnp Yes 3-keto-L-gulonate-6-phosphate C6H8O10P -3 No Kegg entry Neutral-C6H11O10P JLR 498 3dhq No 3-Dehydroquinate C7H9O6 -1 C00944 KEGG - C00944 Neutral MF = C7H10O6 SMP CHS 1199 3dhsk No 3-Dehydroshikimate C7H7O5 -1 10457-99-5 C02637 KEGG - C02637 Neutral MF = C7H8O5 SMP CHS 4601 3gmp Yes 3'-GMP C10H12N5O8P -2 497-76-7 C06193 KEGG - C06193 AMF 988 3haACP Yes (3R)-3-Hydroxyacyl-[acyl-carrier protein] C15H27N2O9PRS -1 C01271 "KEGG - C01271 added formula, renamed from 3R3haprot - NCD JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 905 3hbcoa Yes (S)-3-Hydroxybutanoyl-CoA C25H38N7O18P3S -4 C01144 KEGG - C01144 Neutral MF = C25H42N7O18P3S SMP 26042 3hcddec5eACP Yes (R)-3-hydroxy-cis-dodec-5-enoyl-[acyl-carrier protein] C23H41N2O9PRS -1 AMF 9394 3hcinnm No 3-hydroxycinnamic acid C9H7O3 -1 No Kegg entry see PMID: 9603882 Neutral-C9H8O3 JLR 26040 3hcmrs7eACP Yes (R)-3-hydroxy-cis-myristol-7-eoyl-[acyl-carrier protein] C25H45N2O9PRS -1 AMF 26043 3hcpalm9eACP Yes (R)-3-hydroxy-cis-palm-9-eoyl-[acyl-carrier protein] C27H49N2O9PRS -1 AMF 26044 3hcvac11eACP Yes (R)-3-hydroxy-cis-vacc-11-enoyl-[acyl-carrier protein] C29H53N2O9PRS -1 AMF 3793 3hdcoa Yes (S)-3-Hydroxydecanoyl-CoA C31H50N7O18P3S -4 C05264 KEGG - C05264 Neutral MF = C31H54N7O18P3S SMP 3791 3hddcoa Yes (S)-3-Hydroxydodecanoyl-CoA C33H54N7O18P3S -4 C05262 KEGG - C05262 Neutral MF = C33H58N7O18P3S SMP 4250 3hddecACP Yes (R)-3-Hydroxydodecanoyl-[acyl-carrier protein] C23H43N2O9PRS -1 8/6/7783 C05757 KEGG - C05757 AMF 3303 3hdecACP Yes (R)-3-Hydroxydecanoyl-[acyl-carrier protein] C21H39N2O9PRS -1 320-77-4 C04619 KEGG - C04619 AMF 3797 3hhcoa Yes (S)-3-Hydroxyhexanoyl-CoA C27H42N7O18P3S -4 C05268 KEGG - C05268 Neutral MF = C27H46N7O18P3S SMP 9558 3hhdcoa Yes (S)-3-Hydroxyhexadecanoyl-CoA C37H62N7O18P3S -4 C05258 KEGG - C05258 Neutral MF = C37H66N7O18P3S SMP 11011 3hhexACP Yes (R)-3-Hydroxyhexanoyl-[acyl-carrier protein] C17H31N2O9PRS -1 8/6/7783 C05747 KEGG - C05747 AMF 8352 3hmrsACP No (R)-3-Hydroxytetradecanoyl-[acyl-carrier protein] C25H47N2O9PRS -1 C04688 "Based on NH page 1040 and 615 JLR JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 3795 3hocoa Yes (S)-3-Hydroxyoctanoyl-CoA C29H46N7O18P3S -4 C05266 KEGG - C05266 Neutral MF = C29H50N7O18P3S SMP 10665 3hoctaACP Yes (R)-3-Hydroxyoctadecanoyl-[acyl-carrier protein] C29H55N2O9PRS -1 tv (3/25/03) AMF 25943 3hoctACP Yes (R)-3-Hydroxyoctanoyl-[acyl-carrier protein] C19H35N2O9PRS -1 C04620 AMF 8403 3hodcoa Yes (S)-3-Hydroxyoctadecanoyl-CoA C39H66N7O18P3S -4 NCD 11870 3hpalmACP Yes R-3-hydroxypalmitoyl-[acyl-carrier protein] C27H51N2O9PRS -1 C04633 tv (3/26/03) AMF 9393 3hpppn No 3-(3-hydroxy-phenyl)propionate C9H9O3 -1 No Kegg entry see PMID: 9603882 Neutral JLR 3789 3htdcoa Yes (S)-3-Hydroxytetradecanoyl-CoA C35H58N7O18P3S -4 C05260 KEGG - C05260 Neutral MF = C35H62N7O18P3S SMP 11266 3ig3p No C'-(3-Indolyl)-glycerol 3-phosphate C11H12NO6P -2 C03506 KEGG - C03506 Neutral MF = C11H14NO6P SMP Checked N-groups JLR 225 3mob No 3-Methyl-2-oxobutanoate C5H7O3 -1 C00141 KEGG - C00141 Neutral MF = C5H8O3 SMP CHS 445 3mop No (S)-3-Methyl-2-oxopentanoate C6H9O3 -1 C00671 KEGG - C00671 Neutral MF = C6H10O3 C003465 and C03911 are deleted SMP CHS 26038 3ocddec5eACP Yes 3-oxo-cis-dodec-5-enoyl-[acyl-carrier protein] C23H39N2O9PRS -1 AMF 26039 3ocmrs7eACP Yes 3-oxo-cis-myristol-7-eoyl-[acyl-carrier protein] C25H43N2O9PRS -1 AMF 26045 3ocpalm9eACP Yes 3-oxo-cis-palm-9-eoyl-[acyl-carrier protein] C27H47N2O9PRS -1 AMF 26046 3ocvac11eACP Yes 3-oxo-cis-vacc-11-enoyl-[acyl-carrier protein] C29H51N2O9PRS -1 AMF 3794 3odcoa Yes 3-Oxodecanoyl-CoA C31H48N7O18P3S -4 C05265 KEGG - C05265 Neutral MF = C31H52N7O18P3S SMP 3792 3oddcoa Yes 3-Oxododecanoyl-CoA C33H52N7O18P3S -4 C05263 KEGG - C05263 Neutral MF = C33H56N7O18P3S SMP 4249 3oddecACP Yes 3-Oxododecanoyl-[acyl-carrier protein] C23H41N2O9PRS -1 8/6/7783 C05756 KEGG - C05756 AMF 4247 3odecACP Yes 3-Oxodecanoyl-[acyl-carrier protein] C21H37N2O9PRS -1 8/6/7783 C05753 KEGG - C05753 AMF 3798 3ohcoa Yes 3-Oxohexanoyl-CoA C27H40N7O18P3S -4 5096-70-8 C05269 KEGG - C05269 Neutral MF = C27H44N7O18P3S SMP 3788 3ohdcoa Yes 3-Oxohexadecanoyl-CoA C37H60N7O18P3S -4 C05259 KEGG - C05259 Neutral MF = C37H64N7O18P3S SMP 4242 3ohexACP Yes 3-Oxohexanoyl-[acyl-carrier protein] C17H29N2O9PRS -1 8/6/7783 C05746 KEGG - C05746 AMF 10993 3omrsACP Yes 3-Oxotetradecanoyl-[acyl-carrier protein] C25H45N2O9PRS -1 8/6/7783 C05759 KEGG - C05759 AMF 3796 3oocoa Yes 3-Oxooctanoyl-CoA C29H44N7O18P3S -4 C05267 KEGG - C05267 Neutral MF = C29H48N7O18P3S SMP 4245 3ooctACP Yes 3-Oxooctanoyl-[acyl-carrier protein] C19H33N2O9PRS -1 8/6/7783 C05750 KEGG - C05750 AMF 26130 3ooctdACP Yes 3-Oxooctadecanoyl-[acyl-carrier protein] C29H53N2O9PRS -1 AMF 13976 3oodcoa Yes 3-Oxooctadecanoyl-CoA C39H64N7O18P3S -4 SMP (2/7/03) 4254 3opalmACP Yes 3-Oxohexadecanoyl-[acyl-carrier protein] C27H49N2O9PRS -1 8/6/7783 C05762 KEGG - C05762 AMF 4481 3ophb No 3-Octaprenyl-4-hydroxybenzoate C47H69O3 -1 C05809 KEGG - C05809 Neutral MF = C47H70O3 SMP CHS 3790 3otdcoa Yes 3-Oxotetradecanoyl-CoA C35H56N7O18P3S -4 C05261 KEGG - C05261 Neutral MF = C35H60N7O18P3S SMP 259 3pg No 3-Phospho-D-glycerate C3H4O7P -3 C00197 KEGG - C00197 Neutral MF = C3H7O7P Deleted C00597 SMP CHS 9544 3php No 3-Phosphohydroxypyruvate C3H2O7P -3 C03232 KEGG - C03232 Neutral MF = C3H5O7P SMP CHS 7139 3psme No 5-O-(1-Carboxyvinyl)-3-phosphoshikimate C10H9O10P -4 C01269 KEGG - C01269 Neutral MF = C10H13O10P SMP 1105 3sala Yes 3-Sulfino-L-alanine C3H5NO4S -2 1115-65-7 C00606 KEGG - C00606 Neutral MF = C3H7NO4S SMP CHS 526 3ump Yes 3'-UMP C9H11N2O9P -2 35170-03-7 C01368 KEGG - C01368 AMF 176 4abut No 4-Aminobutanoate C4H9NO2 0 56-12-2 C00334 KEGG - C00334 Neutral MF = C4H9NO2 SMP CHS Changed according to Genomatica JLR 376 4abutn No 4-Aminobutanal C4H10NO 1 C00555 KEGG - C00555 Neutral Compound SMP CHS Changed according to Genomatica JLR 385 4abz No 4-Aminobenzoate C7H6NO2 -1 150-13-0 C00568 KEGG - C00568 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR 6422 4adcho No 4-amino-4-deoxychorismate C10H10NO5 -1 C11355 "KEGG - C11355 MM Neutral MF = C10H11NO5 SMP Note: NH pg 667 has metab drawn incorrectly should be carboxylic not methyl group (pka of N group around 9,using ACD software) Checked N-groups JLR" 992 4ahmmp No 4-Amino-5-hydroxymethyl-2-methylpyrimidine C6H9N3O 0 73-67-6 C01279 KEGG - C01279 Neutral SMP CHS Checked N-groups JLR 3999 4ampm No 4-Amino-2-methyl-5-phosphomethylpyrimidine C6H8N3O4P -2 C04556 KEGG - C04556 Neutral MF = C6H10N3O4P SMP CHS Checked N-groups JLR 6328 4c2me No 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H23N3O14P2 -2 C11435 KEGG C11435 Neutral MF = C14H25N3O14P2 SMP Checked N-groups JLR 2758 4h2opntn No 4-Hydroxy-2-oxopentanoate C5H7O4 -1 111844-33-8 C03589 KEGG - C03589 Neutral-C5H8O4 JLR 5872 4hba No 4-Hydroxy-benzyl alcohol C7H8O2 0 tv 234 4hbz No 4-Hydroxybenzoate C7H5O3 -1 99-96-7 C00156 KEGG - C00156 Neutral MF = C7H6O3 SMP CHS 2887 4hoxpacd Yes 4-Hydroxyphenylacetaldehyde C8H8O2 0 60-11-7 C03765 KEGG - C03765 SAB 8737 4hthr No 4-Hydroxy-L-threonine C4H9NO4 0 C06056 KEGG C06056 JLR Checked N JLR 3272 4mhetz No 4-Methyl-5-(2-hydroxyethyl)-thiazole C6H9NOS 0 137-00-8 C04294 KEGG - C04294 Neutral SMP CHS Checked N-groups JLR 285 4mop No 4-Methyl-2-oxopentanoate C6H9O3 -1 C00233 KEGG - C00233 Neutral MF = C6H10O3 SMP CHS 2627 4mpetz No 4-Methyl-5-(2-phosphoethyl)-thiazole C6H8NO4PS -2 C04327 KEGG - C04327 Neutral MF = C6H10NO4PS SMP CHS Checked N-groups JLR 2319 4pasp No 4-Phospho-L-aspartate C4H6NO7P -2 C03082 KEGG - C03082 Neutral MF = C4H8NO7P SMP CHS Changed according to Genomatica JLR 1954 4per No 4-Phospho-D-erythronate C4H6O8P -3 C03393 KEGG - C03393 Neutral MF = C4H9O8P SMP CHS 2022 4ppan No D-4'-Phosphopantothenate C9H15NO8P -3 C03492 KEGG - C03492 Neutral MF = C9H18NO8P SMP CHS Checked N-groups JLR 2645 4ppcys No N-((R)-4-Phosphopantothenoyl)-L-cysteine C12H20N2O9PS -3 C04352 KEGG - C04352 Neutral MF = C12H23N2O9PS SMP CHS Checked N-groups JLR 3484 4r5au No 4-(1-D-Ribitylamino)-5-aminouracil C9H16N4O6 0 C04732 "KEGG - C04732 SMP Checked N-groups, agrees with ACD software, JLR" 10916 5aizc No 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate C9H11N3O9P -3 C04751 KEGG - C04751 Neutral MF = C9H14N3O9P SMP CHS Checked N-groups JLR 424 5aop No 5-Amino-4-oxopentanoate C5H9NO3 0 106-60-5 C00430 KEGG - C00430 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR 3938 5aprbu No 5-Amino-6-(5'-phosphoribitylamino)uracil C9H15N4O9P -2 C04454 "KEGG - C04454 Neutral MF = C9H17N4O9P SMP Checked N-groups NCD, JLR" 986 5apru No 5-Amino-6-(5'-phosphoribosylamino)uracil C9H13N4O9P -2 C01268 "KEGG - C01268 Neutral MF = C9H15N4O9P SMP Checked N-groups JLR, NCD" 6593 5caiz No 5-phosphoribosyl-5-carboxyaminoimidazole C9H11N3O9P -3 "JLR - could not find the metabolite in KEGG. Metabolite is in Neidhardt,"" Escherichia coli and Salmonella cellular and molecular biology"" 2nd edition, page 563. Used in E. coli purine biosynthesis Checked N-groups JLR" 695 5dglcn No 5-Dehydro-D-gluconate C6H9O7 -1 C01062 KEGG - C01062 Neutral-C6H10O7 JLR 448 5dh4dglc No 5-Dehydro-4-deoxy-D-glucarate C6H6O7 -2 C00679 KEGG - C00679 Neutral-C6H8O7 JLR 3193 5mdr1p No 5-Methylthio-5-deoxy-D-ribose 1-phosphate C6H11O7PS -2 C04188 KEGG - C04188 Neutral MF = C6H13O7PS SMP CHS 3277 5mdru1p No 5-Methylthio-5-deoxy-D-ribulose 1-phosphate C6H11O7PS -2 C04582 KEGG - C04582 Neutral MF = C6H13O7PS SMP CHS 243 5mta No 5-Methylthioadenosine C11H15N5O3S 0 2457-80-9 C00170 KEGG - C00170 Neutral MF = C11H15N5O3S SMP CHS Checked N-groups JLR 431 5mthf No 5-Methyltetrahydrofolate C20H24N7O6 -1 C00440 "KEGG - C00440 Neutral MF = C20H25N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Note that Kegg structure is incorrect, in one of the rings there should be a N rather than a C (see thf) Agrees with pipeline pilot" 2324 5mtr No 5-Methylthio-D-ribose C6H12O4S 0 C03089 KEGG - C03089 Neutral Compound SMP CHS 3520 5prdmbz No "N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole" C14H17N2O7P -2 C04778 KEGG - C04778 Neutral MF = C14H19N2O7P SMP JLR Checked N-groups JLR 8267 6hmhpt No 6-hydroxymethyl dihydropterin C7H9N5O2 0 "JLR- Neidhardt pg 667; different from 2ahhmp because Ketone vs. OH group on nitrogen ring Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked - AMF" 8269 6hmhptpp No 6-hydroxymethyl-dihydropterin pyrophosphate C7H8N5O8P2 -3 "JLR - Neidhardt pg 667, different from 2ahhmd because Ketone vs. OH group on nitrogen ring Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR" 182 6pgc No 6-Phospho-D-gluconate C6H10O10P -3 C00345 KEGG - C00345 Neutral MF = C6H13O10P SMP CHS 963 6pgl No "6-phospho-D-glucono-1,5-lactone" C6H9O9P -2 None C01236 KEGG - C01236 Neutral MF = C6H11O9P SMP CHS 873 8aonn No 8-Amino-7-oxononanoate C9H17NO3 0 C01092 KEGG - C01092 Neutral MF = C9H17NO3 SMP CHS Changed according to Genomatica JLR 4943 aacald No Aminoacetaldehyde C2H6NO 1 452-86-8 C06735 KEGG - C06735 Checked N JLR 174 aacoa No Acetoacetyl-CoA C25H36N7O18P3S -4 1420-36-6 C00332 KEGG - C00332 Neutral MF = C25H40N7O18P3S SMP CHS 1533 aact Yes Aminoacetone C3H8NO 1 298-08-8 C01888 KEGG - C01888 Neutral Compound SMP Checked N-groups JLR 319 ac No Acetate C2H3O2 -1 64-19-7 C00033 KEGG - C00033 Neutral MF = C2H4O2 SMP CHS 9016 acac No Acetoacetate C4H5O3 -1 541-50-4 C00164 KEGG - C00164 NCD 5509 acACP No Acetyl-ACP C13H23N2O8PRS -1 "tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 1052 acald No Acetaldehyde C2H4O 0 75-07-0 C00084 KEGG - C00084 Neutral Compound SMP CHS 4054 acanth Yes N-Acetylanthranilate C9H8NO3 -1 89-52-1 C06332 KEGG - C06332 AMF 11537 accoa No Acetyl-CoA C23H34N7O17P3S -4 72-89-9 C00024 KEGG - C00024 Neutral MF = C23H38N7O17P3S SMP CHS 3775 acetol Yes Acetol C3H6O2 0 116-09-6 C05235 KEGG - C05235 NCD 2957 acg5p No N-Acetyl-L-glutamyl 5-phosphate C7H9NO8P -3 C04133 KEGG - C04133 Neutral MF = C7H12NO8P SMP CHS Checked N-groups JLR 975 acg5sa No N-Acetyl-L-glutamate 5-semialdehyde C7H10NO4 -1 None C01250 KEGG - C01250 Neutral MF = C7H11NO4 SMP CHS Checked N-groups JLR 899 acgal Yes N-Acetyl-D-galactosamine C8H15NO6 0 14215-68-0; 1811-31-0 C01132 KEGG - C01132 Neutral Compound SMP NCD 19195 acgal1p Yes N-Acetyl-D-galactosamine 1-phosphate C8H14NO9P -2 not in KEGG NCD 224 acgam Yes N-Acetyl-D-glucosamine C8H15NO6 0 7512-17-6 C00140 KEGG - C00140 Neutral Compound SMP Checked N-groups JLR 3247 acgam1p No N-Acetyl-D-glucosamine 1-phosphate C8H14NO9P -2 None C04256 KEGG - C04256 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR 192 acgam6p No N-Acetyl-D-glucosamine 6-phosphate C8H14NO9P -2 102029-88-9 C00357 KEGG - C00357 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR 1208 acglc-D Yes 6-Acetyl-D-glucose C8H14O7 0 107-85-7 C02655 KEGG - C02655 AMF 1115 acglu No N-Acetyl-L-glutamate C7H9NO5 -2 1188-37-0 C00624 KEGG - C00624 Neutral MF = C7H11NO5 SMP CHS Checked N-groups JLR 1728 acmalt Yes Acetyl-maltose C14H24O12 0 C02130 KEGG - C02130 Neutral Compound SMP 1129 acmana No N-Acetyl-D-mannosamine C8H15NO6 0 3615-17-6 C00645 KEGG - C00645 Neutral Compound SMP Checked N-groups JLR 11865 acmanap No N-Acetyl-D-mannosamine 6-phosphate C8H14NO9P -2 157296-99-6 C04257 KEGG - C04257 Neutral-C8H16NO9P JLR Checked N JLR 2040 acmum Yes N-Acetylmuramate C11H18NO8 -1 61633-75-8 C02713 KEGG - C02713 JLR Checked N-Groups 12407 acmum6p Yes N-acetylmuramate 6-phosphate C11H17NO11P -3 Not in KEGG see PMID 15060041 JLR AMF 134 acnam No N-Acetylneuraminate C11H18NO9 -1 131-48-6 C00270 KEGG - C00270 Neutral MF = C11H19NO9 SMP CHS Checked N-groups JLR 22094 acolipa Yes 4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A C181H314N3O103P4 -9 AMF 417 acon-C Yes cis-Aconitate C6H3O6 -3 585-84-2 C00417 KEGG - C00417 Neutral MF = C6H6O6 SMP CHS 9959 aconm No E-3-carboxy-2-pentenedioate 6-methyl ester C7H6O6 -2 "Not in Kegg (see PMID 11329290, figure 1) Neutral-C7H8O6 JLR" 1194 acon-T No trans-Aconitate C6H3O6 -3 4023-65-8 C02341 KEGG - C02341 Neutral MF = C6H6O6 SMP CHS 428 acorn No N2-Acetyl-L-ornithine C7H14N2O3 0 None C00437 KEGG - C00437 Neutral MF = C7H14N2O3 SMP CHS Changed according to Genomatica JLR 69 ACP No acyl carrier protein C11H21N2O7PRS -1 C00229 "tv formula deducted by substraction the elemental compositon from (MalACP + CoA) - MalCoA checked with Neidhardt JLR needed to add an H, pka of thiol (-SH) is 9 to 12. JLR changed to include 4-phosphopantetheinyl moiety (see PMID 11867633)" 808 acser No O-Acetyl-L-serine C5H9NO4 0 66638-22-0 C00979 KEGG - C00979 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR 10494 actACP No Acetoacetyl-ACP C15H25N2O9PRS -1 C05744 "tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 281 actp No Acetyl phosphate C2H3O5P -2 19926-71-7 C00227 KEGG - C00227 Neutral MF = C2H5O5P SMP CHS 228 ade No Adenine C5H5N5 0 73-24-5 C00147 KEGG - C00147 Neutral Compound SMP CHS 270 adn No Adenosine C10H13N5O4 0 58-61-7 C00212 KEGG - C00212 Neutral Compound SMP CHS Checked N-groups JLR 5428 adocbi No Adenosyl cobinamide C58H84CoN16O11 1 7625-23-2 C06508 KEGG - C06508 (removed 3 H's from the ring) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 Redone old values were C58H85CoN16O11 with +6 charge (by JLR) 4772 adocbip No Adenosyl cobinamide phosphate C58H83CoN16O14P -1 7625-23-2 C06509 KEGG - C06509 Kegg shows C58H88CoN16O14P (removed 3 H's from the ring and 2 from the phosphate group) JLR before charge was +1 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C58H84CoN16O14P charge +4 (by JLR) 10925 adocbl No Adenosylcobalamin C72H100CoN18O17P 0 13870-90-1 C00194 "KEGG - C00194 Kegg shows C72H105CoN18O17P (removed 3 H from ring, 1H from phosphate group, 1H from ribazole group) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C72H101CoN18O17P charge +7 (by JLR)" 471 adp No ADP C10H12N5O10P2 -3 20398-34-9 C00008 KEGG - C00008 Neutral MF = C10H15N5O10P2 SMP CHS 112 adpglc No ADPglucose C16H23N5O15P2 -2 C00498 KEGG - C00498 Neutral MF = C16H25N5O15P2 SMP CHS 4773 "adphep-D,D" No ADP-D-glycero-D-manno-heptose C17H25N5O16P2 -2 119-61-9 C06397 KEGG - C06397 Neutral-C17H27N5016P2 JLR Checked N JLR 9429 "adphep-L,D" No ADP-L-glycero-D-manno-heptose C17H25N5O16P2 -2 C06398 Kegg- C06398 Neutral-C17H27N5O16P2 JLR Checked N JLR 151 adprib Yes ADPribose C15H21N5O14P2 -2 C00301 KEGG - C00301 Neutral MF = C15H23N5O14P2 SMP CHS checked N groups - NCD 4921 ag Yes silver Ag 1 7440-22-4 C06710 KEGG - C06710 11002 agdpcbi No Adenosine-GDP-cobinamide C68H95CoN21O21P2 -1 7625-23-2 C06510 KEGG - C06510 Kegg shows C68H100CoN21O21P2 (removed 3 H's from ring and 2 from phosphate groups) JLR before charge was +1 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C68H96CoN21O21P2 charge +4 (by JLR) 247 agm No Agmatine C5H16N4 2 306-60-5 C00179 KEGG - C00179 Neutral Compound SMP CHS Changed according to Genomatica JLR 310 ahcys No S-Adenosyl-L-homocysteine C14H20N6O5S 0 979-92-0 C00021 KEGG - C00021 Neutral MF = C14H20N6O5S SMP CHS Changed according to Genomatica JLR 3611 ahdt No "2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate" C9H12N5O13P3 -4 C04895 "KEGG - C04895 Neutral MF = C9H16N5O13P3 SMP Checked N-groups, ACD software indicates a N is protonated, JLR Pipeline Pilot indicates that this N is not protonated. JLR" 3340 aicar No 5-Amino-1-(5-Phospho-D-ribosyl)imidazole-4-carboxamide C9H13N4O8P -2 3031-94-5 C04677 KEGG - C04677 Neutral MF = C9H15N4O8P SMP CHS Checked N-groups JLR 1941 air No 5-amino-1-(5-phospho-D-ribosyl)imidazole C8H12N3O7P -2 25635-88-5 C03373 KEGG - C03373 Neutral MF = C8H14N3O7P SMP CHS Checked N-groups JLR 314 akg No 2-Oxoglutarate C5H4O5 -2 328-50-7 C00026 KEGG - C00026 Neutral MF = C5H6O5 SMP CHS 817 alaala No D-Alanyl-D-alanine C6H12N2O3 0 923-16-0 C00993 KEGG - C00993 Neutral MF = C6H12N2O3 SMP CHS Changed according to Genomatica JLR 1063 ala-B No beta-Alanine C3H7NO2 0 107-95-9 C00099 KEGG - C00099 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR 73 alac-S No (S)-2-Acetolactate C5H7O4 -1 C06010 KEGG - C06010 (C00900 Deleted) Neutral MF = C5H8O4 SMP CHS 1093 ala-D No D-Alanine C3H7NO2 0 338-69-2 C00133 KEGG - C00133 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR 11412 ala-L No L-Alanine C3H7NO2 0 56-41-7 C00041 KEGG - C00041 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR 7096 alatrna Yes L-Alanyl-tRNA(Ala) C3H6NOR 1 C00886 KEGG - C00886 SMP adjusted for Genomatica's change to aa - NCD 2224 all6p Yes D-Allose 6-phosphate C6H11O9P -2 147-94-4 C02962 KEGG - C02962 612 all-D Yes D-Allose C6H12O6 0 2595-97-3 C01487 KEGG - C01487 JLR 1262 alltn No Allantoin C4H6N4O3 0 97-59-6 C01551 KEGG - C01551 Neutral Compound SMP CHS Checked N-groups JLR 113 alltt No Allantoate C4H7N4O4 -1 99-16-1 C00499 KEGG - C00499 Neutral MF = C4H8N4O4 SMP CHS Checked N-groups JLR 15385 allul6p Yes Allulose 6-phosphate C6H11O9P -2 No KEGG entry see allulose and PMID 9401019 JLR 1283 alpp Yes applipoprotein X 0 6244-92-4 C01834 KEGG - C01834 AMF generic lipoprotein for acyl transfering 660 altrn No D-Altronate C6H11O7 -1 C00817 KEGG - C00817 Neutral MF = C6H12O7 No L-altronate found in Chemfinder SMP CHS 1086 amet No S-Adenosyl-L-methionine C15H23N6O5S 1 29908-03-0 C00019 KEGG - C00019 Neutral MF = C15H23N6O5S; neutral form has charge +1 - NCD SMP CHS Changed according to Genomatica JLR 903 ametam No S-Adenosylmethioninamine C14H24N6O3S 2 C01137 KEGG - C01137 SMP Changed according to Genomatica JLR 2693 amob No S-Adenosyl-4-methylthio-2-oxobutanoate C15H19N5O6S 0 C04425 KEGG - C04425 Neutral MF = C15H20N5O6S SMP CHS Checked N-groups JLR 309 amp No AMP C10H12N5O7P -2 61-19-8 C00020 KEGG - C00020 Neutral MF = C10H14N5O7P SMP CHS 21427 anhgm Yes N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid C19H29N2O12 -1 AMF 21428 anhgm3p Yes N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide C34H52N6O19 -2 AMF 21429 anhgm4p Yes N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide C37H57N7O20 -2 AMF 21513 anhm Yes "1,6-anhydrous-N-Acetylmuramate" C11H16NO7 -1 AMF 21511 anhm3p Yes "1,6-anhydrous-N-Acetylmuramyl-tripeptide" C26H39N5O14 -2 AMF 21512 anhm4p Yes "1,6-anhydrous-N-Acetylmuramyl-tetrapeptide" C29H44N6O15 -2 AMF 1070 anth No Anthranilate C7H6NO2 -1 118-92-3 C00108 KEGG - C00108 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR 8976 ap4a No "P1,P4-Bis(5'-adenosyl) tetraphosphate" C20H24N10O19P4 -4 C01260 Kegg- C01260 Neutral-C20H28N10O19P4 JLR 3098 ap5a No "P1,P5-Bis(5'-adenosyl) pentaphosphate" C20H24N10O22P5 -5 4637-56-3 C04058 KEGG - C04058 Neutral-C20H29N10O22P5 JLR 26365 apg120 Yes acyl phosphatidylglycerol (n-C12:0) C42H80O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26366 apg140 Yes acyl phosphatidylglycerol (n-C14:0) C48H92O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26369 apg141 Yes acyl phosphatidylglycerol (n-C14:1) C48H86O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26367 apg160 Yes acyl phosphatidylglycerol (n-C16:0) C54H104O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26370 apg161 Yes acyl phosphatidylglycerol (n-C16:1) C54H98O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26368 apg180 Yes acyl phosphatidylglycerol (n-C18:0) C60H116O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 26371 apg181 Yes acyl phosphatidylglycerol (n-C18:1) C60H110O11P -1 each acyl chain is the same lenght and sam level of saturation AMF 8800 apoACP No apoprotein [acyl carrier protein] RHO 0 JLR 279 aps No Adenosine 5'-phosphosulfate C10H12N5O10PS -2 C00224 KEGG - C00224 Neutral MF = C10H14N5O10PS SMP CHS Checked N-groups JLR 886 ara5p No D-Arabinose 5-phosphate C5H9O8P -2 C01112 KEGG - C01112 neutral MF = C5H11O8P SMP CHS JLR- had incorrect charge should be -2 307 arab-L No L-Arabinose C5H10O5 0 147-81-9 C00259 KEGG - C00259 Neutral Compound SMP CHS 22128 aragund Yes O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C71H115N1O17P2 -2 AMF 4596 arbt6p No Arbutin 6-phosphate C12H15O10P -2 C06187 KEGG - C06187 Neutral MF = C12H17O10P SMP 19380 arbtn Yes aerobactin minus Fe3 C22H33N4O13 -3 0 11290 arbtn-fe3 Yes Aerobactin C22H33FeN4O13 0 61-33-6 C05554 KEGG - C05554 AMF is a siderophore - Fe-scavenging molecule. requires secretion and re-uptake pathways 337 arg-L No L-Arginine C6H15N4O2 1 74-79-3 C00062 KEGG - C00062 Neutral MF = C6H14N4O2 SMP CHS Changed according to Genomatica JLR 1962 argsuc No N(omega)-(L-Arginino)succinate C10H17N4O6 -1 None C03406 KEGG - C03406 Neutral MF = C10H18N4O6 SMP CHS Changed according to Genomatica JLR pKa = 9.58 nitrogen group 7099 argtrna Yes L-Arginyl-tRNA(Arg) C6H14N4OR 2 C02163 KEGG - C02163 SMP adjusted for Genomatica's change to aa - NCD 11868 ascb6p Yes L-ascorbate-6-phosphate C6H7O9P -2 No Kegg Entry JLR 11279 ascb-L Yes L-Ascorbate C6H8O6 0 50-81-7 C00072 KEGG - C00072 JLR 232 asn-L No L-Asparagine C4H8N2O3 0 70-47-3 C00152 KEGG - C00152 Neutral MF = C4H8N2O3 SMP CHS Changed according to Genomatica JLR 7111 asntrna Yes L-Asparaginyl-tRNA(Asn) C4H7N2O2R 1 C03402 KEGG - C03402 SMP adjusted for Genomatica's change to aa - NCD 4908 aso3 Yes arsenite AsO3 -3 C06697 KEGG - C06697 AMF 606 aso4 Yes arsenate AsO4 -3 7778-39-4 C01478 KEGG - C01478 AMF 330 asp-L No L-Aspartate C4H6NO4 -1 56-84-8 C00049 KEGG - C00049 Neutral MF = C4H7NO4 SMP CHS Changed according to Genomatica JLR 432 aspsa No L-Aspartate 4-semialdehyde C4H7NO3 0 None C00441 KEGG - C00441 Neutral MF = C4H7NO3 SMP CHS Changed according to Genomatica JLR 7106 asptrna Yes L-Aspartyl-tRNA(Asp) C4H5NO3R 0 C02984 KEGG - C02984 SMP 3421 athr-L Yes L-Allo-threonine C4H9NO3 0 28954-12-3 C05519 KEGG - C05519 AMF 465 atp No ATP C10H12N5O13P3 -4 56-65-5 C00002 KEGG - C00002 Neutral MF = C10H16N5O13P3 SMP CHS 733 b2coa Yes trans-But-2-enoyl-CoA C25H36N7O17P3S -4 102680-35-3 C00877 KEGG - C00877 Neutral MF = C25H40N7O17P3S SMP 9449 bbtcoa No gamma-butyrobetainyl-CoA C28H46N8O17P3S -3 No Kegg Entry gamma-butyrobetaine with a CoA attached +1 charge on butyrobetaine -4 charge on CoA JLR Checked N-groups JLR 392 betald No Betaine aldehyde C5H12NO 1 C00576 KEGG - C00576 JLR Checked N-groups JLR 22245 bglycogen Yes branching glycogen C6H10O5 0 AMF 556 btal Yes Butanal C4H8O 0 123-72-8 C01412 KEGG - C01412 Neutral Compound SMP 222 btcoa No Butanoyl-CoA C25H38N7O17P3S -4 C00136 KEGG - C00136 Neutral MF = C25H42N7O17P3S SMP 1079 btn No Biotin C10H15N2O3S -1 58-85-5 C00120 KEGG - C00120 Neutral MF = C10H16N2O3S SMP CHS Checked N-groups JLR 9958 btnso No d-biotin d-sulfoxide C10H15N2O4S -1 "Not in Kegg (see PMID 10747793, figure 1) Neutral- C10H16N2O4S JLR Checked N-groups JLR" 294 but No Butyrate (n-C4:0) C4H7O2 -1 107-92-6 C00246 KEGG - C00246 Neutral MF = C4H8O2 SMP changed compound class from peptides - NCD 3236 but2eACP Yes But-2-enoyl-[acyl-carrier protein] C15H25N2O8PRS -1 128-33-6 C04246 KEGG - C04246 AMF 4241 butACP Yes Butyryl-ACP (n-C4:0ACP) C15H27N2O8PRS -1 8/6/7783 C05745 KEGG - C05745 AMF 22149 butso3 Yes butanesulfonate C4H9O3S -1 AMF 8980 camp No cAMP C10H11N5O6P -1 C00575 Kegg C00575 Neutral-C10H12N5O6P JLR 429 cbasp No N-Carbamoyl-L-aspartate C5H6N2O5 -2 C00438 KEGG - C00438 Neutral MF = C5H8N2O5 SMP CHS Checked N-groups JLR 4266 cbi No Cobinamide C48H72CoN11O8 0 1867-62-5 C05774 KEGG - C05774 Kegg shows C48H75CoN11O8 (removed 3H's from ring) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR Note: (Assumed that Co charge is +1 and no hydrogens are removed RM) this was not taken into account for this molecule H75 charge =0 8/2004 REDONE old values were C48H73CoN11O8 charge +5 (by JLR) 10988 cbl1 No Cob(I)alamin C62H88CoN13O14P -1 18534-66-2 C00853 "KEGG - C00853 Kegg shows C62H93CoN13O14P (removed 3 H from ring, 1H from phosphate group, 1H from ribazole group) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR Note: (Updated with Pipeline Pilot Calculations (1 H from the phosphate group removed) RM)-dind't take this into account 8/2004 REDONE old values were C62H89CoN13O14P charge +6 (by JLR)" 11004 cbp No Carbamoyl phosphate CH2NO5P -2 C00169 KEGG - C00169 Neutral MF = CH4NO5P SMP CHS Checked N-groups JLR 13909 cd2 Yes Cadmium Cd 2 C01413 KEGG - C01413 SMP (02/16/03) 26034 cddec5eACP Yes cis-dodec-5-enoyl-[acyl-carrier protein] (n-C12:1) C23H41N2O8PRS -1 AMF 26033 cdec3eACP Yes cis-dec-3-enoyl-[acyl-carrier protein] (n-C10:1) C21H37N2O8PRS -1 AMF 1073 cdp No CDP C9H12N3O11P2 -3 63-38-7 C00112 KEGG - C00112 Neutral MF = C9H15N3O11P2 SMP CHS 26134 cdpdddecg Yes "CDP-1,2-didodecanoylglycerol" C36H63N3O15P2 -2 C00269 KEGG - C00269 AMF 26076 cdpdhdec9eg Yes "CDP-1,2-dihexadec-9-enoylglycerol" C44H75N3O15P2 -2 C00269 AMF 26073 cdpdhdecg Yes "CDP-1,2-dihexadecanoylglycerol" C44H79N3O15P2 -2 C00269 KEGG - C00269 AMF 26077 cdpdodec11eg Yes "CDP-1,2-dioctadec-11-enoylglycerol" C48H83N3O15P2 -2 C00269 AMF 26074 cdpdodecg Yes "CDP-1,2-dioctadecanoylglycerol" C48H87N3O15P2 -2 C00269 AMF 26075 cdpdtdec7eg Yes "CDP-1,2-ditetradec-7-enoylglycerol" C40H67N3O15P2 -2 C00269 AMF 26072 cdpdtdecg Yes "CDP-1,2-ditetradecanoylglycerol" C40H71N3O15P2 -2 C00269 AMF 9376 cechddd No "cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol" C9H11O4 -1 "No Kegg entry, see figure 1 PMID: 9603882 Neutral-C9H12O4 JLR" 9374 cenchddd No "cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol" C9H9O4 -1 No KEGG entry see Figure 1in PMID: 9603882 Neutral-C9H10O4 JLR 7908 cgly Yes Cys-Gly C5H10N2O3S 0 19246-18-5 C01419 KEGG - C01419 NCD changed to protonated form - NCD 1075 chol No Choline C5H14NO 1 62-49-7 C00114 KEGG - C00114 SMP Checked N-groups JLR 299 chor No chorismate C10H8O6 -2 55508-12-8 C00251 KEGG - C00251 Neutral MF = C10H10O6 SMP CHS 419 cinnm No trans-Cinnamate C9H7O2 -1 140-10-3 C00423 KEGG - C00423 Neutral-C9H8O2 JLR 236 cit No Citrate C6H5O7 -3 77-92-9 C00158 KEGG - C00158 Neutral MF = C6H8O7 SMP CHS 169 citr-L No L-Citrulline C6H13N3O3 0 372-75-8 C00327 KEGG - C00327 Neutral MF = C6H13N3O3 SMP CHS Changed according to Genomatica JLR 8744 ckdo No CMP-3-deoxy-D-manno-octulosonate C17H24N3O15P -2 JLR- like KEGG C04121 except ring structure (see NH page 1044) 5268 cl Yes Chloride Cl -1 C00115 0 26137 clpn120 Yes "cardiolipin (tetradodecanoyl, n-C12:0)" C57H108O17P2 -2 C05980 KEGG - C05980 AMF 4430 clpn140 Yes "cardiolipin (tetratetradecanoyl, n-C14:0)" C65H124O17P2 -2 C05980 KEGG - C05980 AMF 26092 clpn141 Yes "cardiolipin (tetratetradec-7-enoyl, n-C14:1)" C65H116O17P2 -2 C05980 KEGG - C05980 AMF 26089 clpn160 Yes "cardiolipin (tetrahexadecanoyl, n-C16:0)" C73H140O17P2 -2 C05980 KEGG - C05980 AMF 26091 clpn161 Yes "cardiolipin (tetrahexadec-9-enoyl, n-C16:1)" C73H132O17P2 -2 C05980 KEGG - C05980 AMF 26090 clpn180 Yes "cardiolipin (tetraoctadecanoyl, n-C18:0)" C81H156O17P2 -2 C05980 KEGG - C05980 AMF 26093 clpn181 Yes "cardiolipin (tetraoctadec-11-enoyl, n-C18:1)" C81H148O17P2 -2 C05980 KEGG - C05980 AMF 11376 cmp No CMP C9H12N3O8P -2 84-52-6 C00055 KEGG - C00055 Neutral MF = C9H14N3O8P SMP CHS 474 co2 No CO2 CO2 0 124-38-9 C00011 KEGG - C00011 Neutral Compound SMP CHS 473 coa No Coenzyme A C21H32N7O16P3S -4 85-61-0 C00010 KEGG - C00010 Neutral MF = C21H36N7O16P3S SMP CHS Checked N JLR Note the H is attached to the S on the CoA 244 cobalt2 Yes Co2+ Co 2 7440-48-4 C00175 KEGG - C00175 22093 colipa Yes core oligosaccharide lipid A C176H303N2O100P4 -11 AMF 26182 cpe160 Yes "cyclopropane phosphatidylethanolamine (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)" C39H74N1O8P1 0 AMF 26183 cpe180 Yes "cyclopropane phosphatidylethanolamine (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)" C43H82N1O8P1 0 AMF 26185 cpg160 Yes "cyclopropane phosphatidylglycerol (dihexadec-9,10-cyclo-anoyl, n-C16:0 cyclo)" C40H74O10P1 -1 AMF 26186 cpg180 Yes "cyclopropane phosphatidylglycerol (dioctadec-11,12-cyclo-anoyl, n-C18:0 cyclo)" C44H82O10P1 -1 AMF 16107 cpgn Yes coprogen C35H52N6O13Fe -1 AMF 22446 cpgn-un Yes coprogen unloaded (no Fe(III)) C35H52N6O13 -4 AMF 2442 cpppg3 No Coproporphyrinogen III C36H40N4O8 -4 2624-63-7 C03263 KEGG - C03263 Deleted C02667 (Coproporphyrinogen) Neutral MF = C36H44N4O8 SMP CHS Checked N-groups JLR 163 crn No L-Carnitine C7H15NO3 0 44985-71-9 C00318 "KEGG - C00318 At neutral pH, this compound is neutral due to positive on nitrogen and negative charge on carboxyl ends. SMP Checked N-groups JLR" 9447 crncoa No L-Carnitinyl-CoA C28H46N8O18P3S -3 No Kegg Entry Carnitine with a CoA attached +1 charge on carnitine -4 charge on CoA JLR Checked N-groups JLR 22160 crn-D Yes D-Carnitine C7H15NO3 0 C00487 KEGG - C00487 AMF 22161 crnDcoa Yes D-carnitinyl-CoA C28H46N8O18P3S -3 AMF 212 csn No Cytosine C4H5N3O 0 71-30-7 C00380 KEGG - C00380 Neutral Compound SMP CHS 3136 ctbt No crotonobetaine C7H13NO2 0 6666-46-2 C04114 "KEGG - C04114 Compound is neutral at pH 7, +1 on N, -1 on O JLR Checked N-groups JLR" 9448 ctbtcoa No crotonobetainyl-CoA C28H44N8O17P3S -3 No Kegg Entry crotonobetaine with a CoA attached +1 charge on crotonobetaine -4 charge on CoA JLR Checked N-groups JLR 338 ctp No CTP C9H12N3O14P3 -4 65-47-4 C00063 KEGG - C00063 Neutral MF = C9H16N3O14P3 SMP CHS 21279 cu Yes Cu+ Cu 1 C00070 5271 cu2 Yes Cu2+ Cu 2 Two entries are made for Cu: Cu3+ and Cu2+ 245 cyan No Hydrogen cyanide CHN 0 57-12-5 C01326 KEGG - C01326 JLR pKa of H attached to C is 9.3 Checked N-groups JLR 560 cynt No Cyanate CNO -1 420-05-3 C01417 KEGG - C01417 Neutral-CHNO JLR Checked N-groups JLR 11128 cys-D Yes D-Cysteine C3H7NO2S 0 921-01-7 C00793 KEGG - C00793 JLR Changed according to Genomatica JLR 1062 cys-L No L-Cysteine C3H7NO2S 0 52-90-4 C00097 KEGG - C00097 Neutral MF = C3H7NO2S SMP CHS Changed according to Genomatica JLR 1150 cyst-L No L-Cystathionine C7H14N2O4S 0 56-88-2 C02291 KEGG - C02291 Neutral MF = C7H14N2O4S SMP CHS Changed according to Genomatica JLR 7109 cystrna Yes L-Cysteinyl-tRNA(Cys) C3H6NOSR 1 C03125 KEGG - C03125 SMP adjusted for Genomatica's change to aa - NCD 92 cytd No Cytidine C9H13N3O5 0 65-46-3 C00475 KEGG - C00475 Neutral Compound SMP CHS Checked N-groups JLR 380 dad-2 No Deoxyadenosine C10H13N5O3 0 958-09-8 C00559 KEGG - C00559 Neutral Compound SMP CHS Checked N-groups JLR 3751 dad-5 Yes 5'-Deoxyadenosine C10H13N5O3 0 C05198 KEGG - C05198 Neutral Compound SMP CHS 265 dadp No dADP C10H12N5O9P2 -3 None C00206 KEGG - C00206 Neutral MF = C10H15N5O9P2 SMP CHS 193 damp No dAMP C10H12N5O6P -2 653-63-4 C00360 KEGG - C00360 Neutral MF = C10H14N5O6P SMP CHS 676 dann No "7,8-Diaminononanoate" C9H21N2O2 1 C01037 KEGG - C01037 Neutral MF = C9H20N2O2 SMP CHS Changed according to Genomatica JLR 1091 datp No dATP C10H12N5O12P3 -4 1927-31-7 C00131 KEGG - C00131 Neutral MF = C10H16N5O12P3 SMP CHS 10 db4p No "3,4-dihydroxy-2-butanone 4-phosphate" C4H7O6P -2 No KEGG Entry Neutral MF = C4H9O6P SMP 3804 dc2coa Yes trans-Dec-2-enoyl-CoA C31H48N7O17P3S -4 C05275 KEGG - C05275 Neutral MF = C31H52N7O17P3S SMP 1277 dca Yes Decanoate (n-C10:0) C10H19O2 -1 334-48-5 C01571 "KEGG - C01571 Neutral MF = C10H20O2 SMP saturated fatty acid, 10 carbons changed compound class from peptide to fatty acid - NCD" 7929 dcaACP Yes Decanoyl-ACP (n-C10:0ACP) C21H39N2O8PRS -1 C05755 "JLR- saturated fatty acid, 10 carbons attached to ACP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 3803 dcacoa Yes Decanoyl-CoA (n-C10:0CoA) C31H50N7O17P3S -4 C05274 KEGG - C05274 Neutral MF = C31H54N7O17P3S SMP 2908 dcamp No "N6-(1,2-Dicarboxyethyl)-AMP" C14H14N5O11P -4 C03794 KEGG - C03794 Neutral MF = C14H18N5O11P SMP CHS Checked N-groups JLR 5272 dcdp No dCDP C9H12N3O10P2 -3 None C00705 KEGG - C00705 Neutral MF = C9H15N3O10P2 SMP CHS 290 dcmp No dCMP C9H12N3O7P -2 1032-65-1 C00239 KEGG - C00239 Neutral MF = C9H14N3O7P SMP CHS 78 dctp No dCTP C9H12N3O13P3 -4 2056-98-6 C00458 KEGG - C00458 Neutral MF = C9H16N3O13P3 SMP CHS 10918 dcyt No Deoxycytidine C9H13N3O4 0 951-77-9 C00881 KEGG - C00881 Neutral Compound SMP CHS Checked N-groups JLR 2416 dd2coa Yes trans-Dodec-2-enoyl-CoA C33H52N7O17P3S -4 C03221 KEGG - C03221 Neutral MF = C33H56N7O17P3S SMP 1919 ddca Yes Dodecanoate (n-C12:0) C12H23O2 -1 143-07-7 C02679 "KEGG - C02679 Neutral MF = C12H24O2 SMP saturated fatty acid, 12 carbons changed compound class from peptides to fatty acid - NCD" 10497 ddcaACP No Dodecanoyl-ACP (n-C12:0ACP) C23H43N2O8PRS -1 C05223 "KEGG C05223 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 1383 ddcacoa Yes Dodecanoyl-CoA (n-C12:0CoA) C33H54N7O17P3S -4 6244-92-4 C01832 KEGG - C01832 Neutral MF = C33H58N7O17P3S SMP 194 dgdp No dGDP C10H12N5O10P2 -3 C00361 KEGG - C00361 Neutral MF=C10H15N5O10P2 CHS 195 dgmp No dGMP C10H12N5O7P -2 902-04-5 C00362 KEGG - C00362 Neutral MF = C10H14N5O7P SMP CHS 172 dgsn No Deoxyguanosine C10H13N5O4 0 961-07-9 C00330 KEGG - C00330 Neutral Compound SMP CHS Checked N-groups JLR 143 dgtp No dGTP C10H12N5O13P3 -4 2564-35-4 C00286 KEGG - C00286 Neutral MF = C10H16N5O13P3 SMP CHS 251 dha No Dihydroxyacetone C3H6O3 0 96-26-4 C00184 KEGG - C00184 1072 dhap No Dihydroxyacetone phosphate C3H5O6P -2 57-04-5 C00111 KEGG - C00111 Neutral MF = C3H7O6P SMP CHS 9379 dhcinnm No "2,3-dihydroxicinnamic acid" C9H7O4 -1 No Kegg entry see figure 1 PMID: 9603882 Neutral-C9H8O4 JLR 10505 dhf No "7,8-Dihydrofolate" C19H19N7O6 -2 4033-27-6 C00415 "KEGG - C00415 Neutral MF = C19H21N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR" 22235 dhmptp Yes dihydromonapterin-triphosphate C9H12N5O13P3 -4 AMF 2809 dhna No "1,4-Dihydroxy-2-naphthoate" C11H7O4 -1 C03657 KEGG - C03657 Neutral MF = C11H8O4 SMP CHS 3592 dhnpt No Dihydroneopterin C9H13N5O4 0 C04874 "KEGG - C04874 SMP CHS Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked - AMF" 177 dhor-S No (S)-Dihydroorotate C5H5N2O4 -1 5988-19-2 C00337 KEGG - C00337 Neutral MF = C5H6N2O4 SMP Checked N-groups JLR 8264 dhpmp No Dihydroneopterin monophosphate C9H12N5O7P -2 C05925 "KEGG - C05925 MM JLR- Neidhardt pg 667 Checked N-groups, ACD indicates that the N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked AMF" 3088 dhpppn No "3-(2,3-Dihydroxyphenyl)propanoate" C9H9O4 -1 145-14-2 C04044 KEGG - C04044 Neutral-C9H10O4 JLR 663 dhpt No Dihydropteroate C14H13N6O3 -1 C00921 "KEGG - C00921 Neutral MF = C14H14N6O3 SMP CHS Checked N-groups, agrees with ACD software JLR" 9537 dhptd No "4,5-dihydroxy-2,3-pentanedione" C5H8O4 0 C11838 KEGG C11838 See PMID: 11489131 JLR 1032 didp Yes dIDP C10H11N4O10P2 -3 C01344 KEGG - C01344 Neutral MF = C10H14N4O10P2 SMP CHS 9639 dimp Yes dIMP C10H11N4O7P -2 C06196 KEGG - C06196 (figure in Kegg is inconsistent with other inosine bases) IT Neutral MF = C10H15N4O7P SMP CHS 3417 din No Deoxyinosine C10H12N4O4 0 890-38-0 C05512 KEGG - C05512 Neutral Compound SMP CHS Checked N-groups JLR 1033 ditp Yes dITP C10H11N4O13P3 -4 66701-25-5 C01345 KEGG - C01345 Neutral MF = C10H15N4O13P3 SMP CHS 8766 dkmpp No "2,3-diketo-5-methylthio-1-phosphopentane" C6H9O6PS -2 JLR- no kegg entry 2342 dmbzid No "5,6-Dimethylbenzimidazole" C9H10N2 0 582-60-5 C03114 KEGG - C03114 SMP JLR Checked N-groups JLR 2629 dmlz No "6,7-Dimethyl-8-(1-D-ribityl)lumazine" C13H18N4O6 0 C04332 "KEGG - C04332 Neutral Compound SMP CHS Checked N-groups, agrees with ACD software, JLR, NCD" 38 dmpp No Dimethylallyl diphosphate C5H9O7P2 -3 358-71-4 C00235 KEGG - C00235 Neutral MF = C5H12O7P2 SMP CHS 395 dms No Dimethyl sulfide C2H6S 0 75-18-3 C00580 KEGG - C00580 9065 dmso No Dimethyl sulfoxide C2H6OS 0 C11143 KEGG C11143 JLR 724 dnad No Deamino-NAD+ C21H24N6O15P2 -2 C00857 KEGG - C00857 Neutral MF = C21H27N6O15P2 SMP Checked N-groups JLR 2882 dopa Yes Dopamine C8H12NO2 1 51-61-6 C03758 KEGG - C03758 SAB 737 dpcoa No Dephospho-CoA C21H33N7O13P2S -2 C00882 KEGG - C00882 Neutral MF = C21H35N7O13P2S SMP CHS Checked N-groups JLR 26278 dsbaox Yes periplasmic protein disulfide isomerase I (oxidized) X 0 AMF 26277 dsbard Yes periplasmic protein disulfide isomerase I (reduced) XH2 0 AMF 26282 dsbcox Yes protein disulfide isomerase II (oxidized) X 0 AMF 26279 dsbcrd Yes protein disulfide isomerase II (reduced) XH2 0 AMF 26283 dsbdox Yes fused thiol:disulfide interchange protein (oxidized) X 0 AMF 26280 dsbdrd Yes fused thiol:disulfide interchange protein (reduced) XH2 0 AMF 26284 dsbgox Yes periplasmic disulfide isomerase/thiol-disulphide oxidase (oxidized) X 0 AMF 26281 dsbgrd Yes periplasmic disulfide isomerase/thiol-disulphide oxidase (reduced) XH2 0 AMF 2542 dscl Yes dihydrosirohydrochlorin C42H41N4O16 -7 65207-12-7 C02463 "KEGG - C02463 Neutral MF = C42H48N4O16 SMP Checked N-groups, agrees with ACD software, JLR" 10716 dtbt No Dethiobiotin C10H17N2O3 -1 C01909 KEGG - C01909 Neutral MF = C10H18N2O3 SMP CHS Checked N-groups JLR 196 dtdp No dTDP C10H13N2O11P2 -3 C00363 KEGG - C00363 Neutral MF = C10H16N2O11P2 SMP CHS 9095 dtdp4aaddg No "dTDP-4-acetamido-4,6-dideoxy-D-galactose" C18H27N3O15P2 -2 No Kegg entry (similar to C04268 excent amino group on sugar is has an acetyl group on it) Neutral-C18H29N3O15P2 JLR Checked N-groups JLR 3064 dtdp4addg No "dTDP-4-amino-4,6-dideoxy-D-glucose" C16H26N3O14P2 -1 157296-99-6 C04268 KEGG - C04268 Neutral-C16H25N3O14P2 JLR Checked N-groups JLR 453 dtdp4d6dg No dTDP-4-dehydro-6-deoxy-D-glucose C16H22N2O15P2 -2 C00687 KEGG - C00687 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR 11394 dtdp4d6dm No dTDP-4-dehydro-6-deoxy-L-mannose C16H22N2O15P2 -2 C00688 KEGG - C00688 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR 712 dtdpglu No dTDPglucose C16H24N2O16P2 -2 2009-24-7 C00842 KEGG - C00842 Neutral-C16H26N2O16P2 JLR Checked N-groups JLR 2288 dtdprmn No dTDP-L-rhamnose C16H24N2O15P2 -2 572-96-3 C03319 KEGG - C03319 Neutral-C16H26N2O15P2 JLR Checked N-groups JLR 197 dtmp No dTMP C10H13N2O8P -2 365-07-1 C00364 KEGG - C00364 Neutral MF = C10H15N2O8P Thymine is normally found as a deoxyriboside SMP CHS 79 dttp No dTTP C10H13N2O14P3 -4 C00459 KEGG - C00459 Neutral MF = C10H17N2O14P3 SMP CHS 1034 dudp No dUDP C9H11N2O11P2 -3 C01346 KEGG - C01346 Neutral MF = C9H14N2O11P2 SMP CHS 198 dump No dUMP C9H11N2O8P -2 964-26-1 C00365 KEGG - C00365 Neutral MF = C9H13N2O8P SMP CHS 355 duri No Deoxyuridine C9H12N2O5 0 951-78-0 C00526 KEGG - C00526 Neutral Compound SMP CHS Checked N-groups JLR 80 dutp No dUTP C9H11N2O14P3 -4 C00460 KEGG - C00460 Neutral MF = C9H15N2O14P3 SMP CHS 5780 dxyl No 1-deoxy-D-xylulose C5H10O4 0 C06257 KEGG C06257 tv Neidhardt pg 683 6320 dxyl5p No 1-deoxy-D-xylulose 5-phosphate C5H9O7P -2 C11437 KEGG C11437 Used by enzymes (EC 4.1.3.37 & 1.1.1.267) Neutral MF = C5H11O7P SMP 10791 e4p No D-Erythrose 4-phosphate C4H7O7P -2 585-18-2 C00279 KEGG - C00279 Neutral MF = C4H9O7P SMP CHS 22117 eca2und Yes (enterobacterial common antigen)x2 undecaprenyl-diphosphate C103H162N6O37P2 -4 AMF 22118 eca3und Yes (enterobacterial common antigen)x3 undecaprenyl-diphosphate C127H198N9O52P2 -5 AMF 22120 eca4colipa Yes (enterobacterial common antigen)x4 core oligosaccharide lipid A C272H447N14O160P4 -15 AMF 22119 eca4und Yes (enterobacterial common antigen)x3 undecaprenyl-diphosphate C151H234N12O67P2 -6 AMF 2677 eig3p No D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate C6H9N2O6P -2 C04666 KEGG - C04666 Neutral MF = C6H11N2O6P SMP CHS Checked N-groups JLR 22025 enlipa Yes phosphoethanolamine KDO(2)-lipid (A) C112H202N3O42P3 -6 AMF 11862 enter No Enterochelin C30H27N3O15 0 "Similar to KEGG - C05821 The side chains should be the same, in Kegg one has an alcohol instead of a ketone. See PMID 9214294 for picture. JLR" 254 etha No Ethanolamine C2H8NO 1 141-43-5 C00189 KEGG - C00189 Checked N-groups JLR 22148 ethso3 Yes ethanesulfonate C2H5O3S -1 AMF 87 etoh No Ethanol C2H6O 0 64-17-5 C00469 KEGG - C00469 Neutral Compound SMP CHS 2235 f1p No D-Fructose 1-phosphate C6H11O9P -2 15978-08-2 C02976 KEGG - C02976 Merged with KEGG - C01094 Neutral MF = C6H13O9P SMP CHS 1053 f6p No D-Fructose 6-phosphate C6H11O9P -2 643-13-0 C00085 KEGG - C00085 Neutral MF = C6H13O9P SMP CHS 478 fad No Flavin adenine dinucleotide oxidized C27H31N9O15P2 -2 146-14-5 C00016 "KEGG - C00016 Neutral MF = C27H33N9O15P2 (FAD) SMP Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD" 42 fadh2 No Flavin adenine dinucleotide reduced C27H33N9O15P2 -2 C01352 "KEGG - C01352 Neutral MF = C27H35N9O15P2 (FADH2) SMP Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD" 340 fald Yes Formaldehyde CH2O 0 50-00-0 C00067 KEGG - C00067 Neutral Compound SMP CHS 878 fc1p No L-Fuculose 1-phosphate C6H11O8P -2 None C01099 "KEGG - C01099 Neutral MF = C6H13O8P SMP NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR" 43 fcl-L No L-fuculose C6H12O5 0 C01721 "KEGG - C01721 Neutral Compound SMP CHS NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR" 189 fdp No "D-Fructose 1,6-bisphosphate" C6H10O12P2 -4 488-69-7 C00354 KEGG - C00354 Neutral MF = C6H14O12P2 SMP CHS 312 fe2 No Fe2+ Fe 2 None C00023 KEGG - C00023 Neutral Compound SMP CHS 5267 fe3 Yes Fe3+ Fe 3 None Neutral Compound SMP CHS 4627 fe3dcit Yes Fe(III)dicitrate C12H10FeO14 -3 90-02-8 C06229 KEGG - C06229 AMF- not sure if any h complexed with iron or carboxyls 22289 fe3dhbzs Yes "ferric 2,3-dihydroxybenzoylserine" C10H10NO6Fe 2 AMF 4626 fe3hox Yes Fe(III)hydroxamate C9H18O6N3Fe 0 C06227 "KEGG - C06227 formula corrected, 3/24/05 MKA contains ""R"" groups - replaced with ethyl groups " 19375 fe3hox-un Yes "Fe(III)hydoxamate, unloaded" C9H18O6N3 -3 "not produced by K-12 ecoli formula not certain - contains ""R"" group (replaced w/ ethyl groups); Fe(III)hydroxamate chemistry unclear, but must lose Fe within cell to be recycled MKA" 9616 fecrm Yes Ferrichrome C27H42FeN9O12 0 90-02-8 C06228 KEGG - C06228 AMF CHEMID (015630645) 19379 fecrm-un Yes Ferrichrome minus Fe(III) C27H42N9O12 -3 CHEMID (015630645) 4628 feenter Yes Fe-enterobactin C30H27FeN3O15 3 90-02-8 C06230 KEGG - C06230 16013 feoxam Yes ferroxamine C25H46FeN6O8 1 C07597 AMF 19381 feoxam-un Yes ferroxamine minus Fe(3) C25H46N6O8 -2 siderophore 2663 fgam No N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide C8H13N2O9P -2 C04376 KEGG - C04376 Neutral MF = C8H15N2O9P SMP CHS Checked N-groups JLR 2153 fldox Yes flavodoxin (oxidized) X 0 121-69-7 C02869 KEGG - C02869 2062 fldrd Yes flavodoxin (reduced) XH2 0 358-71-4 C02745 KEGG - C02745 2465 fmettrna Yes N-Formylmethionyl-tRNA C6H9NO2SR 0 C03294 KEGG - C03294 SMP 336 fmn No FMN C17H19N4O9P -2 146-17-8 C00061 "KEGG - C00061 Neutral MF = C17H21N4O9P SMP CHS Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD" 9453 fmnh2 Yes Reduced FMN C17H21N4O9P -2 67-63-0 KEGG - C01847 Neutral-C17H23N4O9P JLR 334 for No Formate CH1O2 -1 64-18-6 C00058 KEGG - C00058 Neutral MF = CH2O2 SMP CHS 3319 fpram No 2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine C8H15N3O8P -1 C04640 KEGG - C04640 Neutral MF = C8H16N3O8P SMP CHS Changed according to Genomatica JLR 3486 fprica No 5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide C10H13N4O9P -2 C04734 KEGG - C04734 Neutral MF = C10H15N4O9P SMP Checked N-groups JLR 10388 frdp No Farnesyl diphosphate C15H25O7P2 -3 13058-04-3 C00448 KEGG - C00448 Neutral MF = C15H28O7P2 SMP 1061 fru No D-Fructose C6H12O6 0 57-48-7 C00095 KEGG - C00095 Deleted KEGG -C01496 (fructose) Neutral Compound SMP CHS 17892 frulys Yes fructoselysine C12H25N2O7 1 MKA 17998 frulysp Yes fructoselysine Phosphate C12H24N2O10P -1 MKA AMF 750 fruur No D-Fructuronate C6H9O7 -1 669-90-9 C00905 KEGG - C00905 Neutral MF = C6H10O7 SMP CHS 2240 fuc1p-L No L-Fucose 1-phosphate C6H11O8P -2 526-31-8 C02985 KEGG - C02985 Neutral-C6H13O8P JLR 833 fuc-L No L-Fucose C6H12O5 0 2438-80-4 C01019 KEGG - C01019 Neutral Compound SMP 1081 fum No Fumarate C4H2O4 -2 110-17-8 C00122 KEGG - C00122 Neutral MF = C4H4O4 SMP CHS 1066 g1p No D-Glucose 1-phosphate C6H11O9P -2 59-56-3 C00103 KEGG - C00103 Neutral MF = C6H13O9P SMP CHS 438 g3p No Glyceraldehyde 3-phosphate C3H5O6P -2 142-10-9 C00661 "KEGG - C00661 Neutral MF = C3H7O6P SMP CHS JLR (deleted duplicate entry, Dglyad3p. g3p should be KEGG- C00118)" 444 g3pc No sn-Glycero-3-phosphocholine C8H20NO6P 0 C00670 KEGG - C00670 Normally has a + charge (C8H21NO6P) JLR 961 g3pe No sn-Glycero-3-phosphoethanolamine C5H14NO6P 0 C01233 KEGG - C01233 Neutral-C5H14NO6P JLR Checked N JLR 2449 g3pg No Glycerophosphoglycerol C6H14O8P -1 11034-93-8 C03274 KEGG - C03274 Neutral-C6H15O8P JLR 954 g3pi No sn-Glycero-3-phospho-1-inositol C9H18O11P -1 C01225 KEGG - C01225 Neutral-C9H19O11P JLR 8967 g3ps No Glycerophosphoserine C6H13NO8P -1 No Kegg entry Neutral-C6H14NO8P JLR Checked N JLR 765 g6p No D-Glucose 6-phosphate C6H11O9P -2 56-73-5 C00092 KEGG - C00092 Neutral MF = C6H13O9P SMP CHS 22090 gagicolipa Yes galactosyl-glucosyl-inner core oligosaccharide lipid A C157H271N2O84P4 -11 AMF 1083 gal No D-Galactose C6H12O6 0 59-23-4 C00124 KEGG - C00124 Deleted KEGG - C01582 (Galactose) Neutral Compound SMP CHS 434 gal1p No alpha-D-Galactose 1-phosphate C6H11O9P -2 2255-14-3 C00446 KEGG - C00446 Neutral MF = C6H13O9P SMP CHS 1002 gal-bD Yes beta D-Galactose C6H12O6 0 33419-42-0 C01582 KEGG - C01582 NCD 735 galct-D No D-Galactarate C6H8O8 -2 526-99-8 C00879 KEGG - C00879 Neutral-C6H10O8 JLR 736 galctn-D No D-Galactonate C6H11O7 -1 C00880 KEGG - C00880 Neutral-C6H12O7 JLR 1377 galt Yes Galactitol C6H14O6 0 608-66-2 C01697 KEGG - C01697 Neutral Compound SMP 6457 galt1p No Galactitol 1-phosphate C6H13O9P -2 C06311 KEGG- C06311 Neutral MF = C6H15O9P JLR 175 galur No D-Galacturonate C6H9O7 -1 685-73-4 C00333 KEGG - C00333 Neutral MF = C6H10O7 SMP CHS 171 gam Yes D-Glucosamine C6H14NO5 1 3416-24-8 C00329 KEGG - C00329 Neutral Compound SMP CHS Changed according to Genomatica JLR 4572 gam1p No D-Glucosamine 1-phosphate C6H13NO8P -1 C06156 KEGG - C06156 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR 187 gam6p No D-Glucosamine 6-phosphate C6H13NO8P -1 3616-42-0 C00352 KEGG - C00352 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR 10804 gar No N1-(5-Phospho-D-ribosyl)glycinamide C7H14N2O8P -1 C03838 KEGG - C03838 Neutral MF = C7H15N2O8P SMP CHS Changed according to Genomatica JLR 22129 garagund Yes glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C77H125N1O22P2 -2 AMF 9450 gbbtn No gamma-butyrobetaine C7H15NO2 0 "No Kegg entry, it is in EcoCyc Compound is a zwitterion, + charge on N and - charge on O JLR Checked N-groups JLR" 10800 gcald No Glycolaldehyde C2H4O2 0 C00266 KEGG - C00266 SMP CHS 321 gdp No GDP C10H12N5O11P2 -3 146-91-8 C00035 KEGG - C00035 Neutral MF = C10H15N5O11P2 SMP CHS 952 gdpddman No GDP-4-dehydro-6-deoxy-D-mannose C16H21N5O15P2 -2 C01222 KEGG - C01222 Neutral: C16H23N5O15P2 JLR Checked N-groups JLR 168 gdpfuc No GDP-L-fucose C16H23N5O15P2 -2 C00325 KEGG - C00325 KEGG glycan: G10615 Neutral: C16H25N5O15P2 JLR 9064 gdpmann No GDP-D-mannose C16H23N5O16P2 -2 C00096 KEGG C00096 Neutral:C16H25N5O16P2 JLR Checked N-groups JLR 3889 gdpofuc No GDP-4-oxo-L-fucose C16H21N5O15P2 -2 583-08-4 C05389 KEGG - C05389 Neutral: C16H23N5O15P2 JLR Checked N-Groups JLR 3963 gdptp Yes Guanosine 3'-diphosphate 5'-triphosphate C10H11N5O20P5 -7 C04494 KEGG - C04494 Neutral MF = C10H18N5O20P5 SMP CHS 22130 gfgaragund Yes galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C83H135N1O27P2 -2 AMF 18600 gg4abut Yes gamma-glutamyl-gamma aminobutyric acid C9H15O5N2 -1 MKA 22091 ggagicolipa Yes glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C163H281N2O89P4 -11 AMF 18597 ggbutal Yes gamma-glutamyl-gamma-butyraldehyde C9H16O4N2 0 MKA 22092 gggagicolipa Yes glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C169H291N2O94P4 -11 AMF 18596 ggptrc Yes gamma-glutamyl-putrescine C9H20O3N3 1 MKA AMF 22089 gicolipa Yes glucosyl-inner core oligosaccharide lipid A C151H261N2O79P4 -11 AMF 318 glc-D No D-Glucose C6H12O6 0 50-99-7 C00031 KEGG - C00031 Deleted KEGG - C00267 (alpha-D-Glucose) Deleted KEGG - C00221 (beta-D-Glucose) L-glucose is abbreviated as glc-L SMP CHS 305 glcn No D-Gluconate C6H11O7 -1 526-95-4 C00257 KEGG - C00257 Neutral MF = C6H12O7 SMP CHS 632 glcr No D-Glucarate C6H8O8 -2 87-73-0 C00818 KEGG - C00818 KEGG - C00767 has Glucarate is deleted from the database Neutral MF = C6H10O8 SMP CHS 256 glcur No D-Glucuronate C6H9O7 -1 12/3/6556 C00191 KEGG - C00191 Neutral MF = C6H10O7 SMP CHS 3887 glcur1p Yes D-Glucuronate 1-phosphate C6H8O10P -3 583-08-4 C05385 KEGG - C05385 NCD 11299 gln-L No L-Glutamine C5H10N2O3 0 56-85-9 C00064 KEGG - C00064 Neutral MF = C5H10N2O3 SMP CHS 7100 glntrna Yes L-Glutaminyl-tRNA(Gln) C5H9N2O2R 1 C02282 KEGG - C02282 SMP adjusted for Genomatica's change to aa - NCD 2004 glu1sa No L-Glutamate 1-semialdehyde C5H9NO3 0 None C03741 KEGG - C03741 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR 2458 glu5p No L-Glutamate 5-phosphate C5H8NO7P -2 C03287 KEGG - C03287 Neutral MF = C5H10NO7P SMP Changed according to Genomatica JLR 761 glu5sa No L-Glutamate 5-semialdehyde C5H9NO3 0 None C01165 KEGG - C01165 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR 443 glucys No gamma-L-Glutamyl-L-cysteine C8H13N2O5S -1 686-58-8 C00669 KEGG - C00669 Neutral MF = C8H14N2O5S SMP CHS Changed according to Genomatica JLR 273 glu-D No D-Glutamate C5H8NO4 -1 56-86-0 C00217 KEGG - C00217 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR 313 glu-L No L-Glutamate C5H8NO4 -1 56-86-0 C00025 KEGG - C00025 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR 2242 glutrna No L-Glutamyl-tRNA(Glu) C5H7NO3R 0 None C02987 "KEGG - C02987 X = (C5H8O6PR)n Represent as neutral SMP; MF changed on May 7, 2002 CHS Changed according to Genomatica JLR" 329 glx No Glyoxylate C2H1O3 -1 298-12-4 C00048 KEGG - C00048 Neutral MF = C2H2O3 SMP CHS 323 gly No Glycine C2H5NO2 0 56-40-6 C00037 KEGG - C00037 Nonchiral compound Neutral MF = C2H5NO2 SMP CHS Changed according to Genomatica JLR 393 glyald No D-Glyceraldehyde C3H6O3 0 453-17-8 C00577 KEGG - C00577 KEGG has non-chiral glyceraldehyde (367-47-5) Neutral Compound SMP CHS 503 glyb No Glycine betaine C5H11NO2 0 107-43-7 C00719 KEGG - C00719 SMP Checked N-groups JLR 1077 glyc No Glycerol C3H8O3 0 56-81-5 C00116 KEGG - C00116 Neutral Compound SMP CHS 2237 glyc2p Yes Glycerol 2-phosphate C3H7O6P -2 3249-68-1 C02979 KEGG - C02979 AMF 55 glyc3p No Glycerol 3-phosphate C3H7O6P -2 C00093 KEGG - C00093 Neutral MF = C3H9O6P SMP 237 glyclt No Glycolate C2H3O3 -1 79-14-1 C00160 KEGG - C00160 Neutral MF = C2H4O3 SMP CHS 5796 glycogen No glycogen C6H10O5 0 C00182 "KEGG- C00182 MF revised on May-7-2002 Deleted previous entry ""glcgn"" Polymer with unit MF = C6H10O5 SMP" 306 glyc-R No (R)-Glycerate C3H5O4 -1 473-81-4 C00258 KEGG - C00258 Neutral MF = C3H6O4 SMP CHS 7101 glytrna Yes Glycyl-tRNA(Gly) C2H4NOR 1 C02412 KEGG - C02412 SMP adjusted for Genomatica's change to aa - NCD 9431 gmhep17bp No "D-Glycero-D-manno-heptose 1,7-bisphosphate" C7H12O13P2 -4 C11472 Kegg C11472 Neutral- C7H16O13P2 JLR 9430 gmhep1p No D-Glycero-D-manno-heptose 1-phosphate C7H13O10P -2 C07838 KEGG C07838 Neutral C7H15O10P 9434 gmhep7p No D-Glycero-D-manno-heptose 7-phosphate C7H13O10P -2 C07836 Kegg C07836 Neutral-C7H15O10P JLR 226 gmp No GMP C10H12N5O8P -2 85-32-5 C00144 KEGG - C00144 Neutral = C10H14N5O8P SMP CHS 8979 gp4g No "P1,P4-Bis(5'-guanosyl) tetraphosphate" C20H24N10O21P4 -4 C01261 Kegg- C01261 Neutral-C20H28N10O21P4 JLR 179 grdp No Geranyl diphosphate C10H17O7P2 -3 C00341 KEGG - C00341 Neutral MF = C10H20O7P2 SMP 22268 grxox Yes glutaredoxin (oxidized) X 0 AMf C07293 22267 grxrd Yes glutaredoxin (reduced) XH2 0 AMF C07292 5279 gsn No Guanosine C10H13N5O5 0 118-00-3 C00387 KEGG - C00387 Neutral Compound SMP CHS Checked N-groups JLR 1087 gthox No Oxidized glutathione C20H30N6O12S2 -2 C00127 KEGG - C00127 Neutral MF = C20H32N6O12S2 SMP CHS Changed according to Genomatica JLR 11388 gthrd No Reduced glutathione C10H16N3O6S -1 70-18-8 C00051 KEGG - C00051 Neutral MF = C10H17N3O6S SMP CHS Changed according to Genomatica JLR 327 gtp No GTP C10H12N5O14P3 -4 86-01-1 C00044 KEGG - C00044 Neutral MF = C10H16N5O14P3 SMP CHS 4235 gtspmd No Glutathionylspermidine C17H36N6O5S 2 8/6/7783 C05730 KEGG - C05730 Neutral-C17H34N6O5S JLR Checked N-groups JLR 291 gua No Guanine C5H5N5O 0 73-40-5 C00242 KEGG - C00242 Neutral Compound SMP CHS 1049 h No H+ H 1 12408-02-5 C00080 KEGG - C00080 141 h2 No H2 H2 0 1333-74-0 C00282 KEGG - C00282 8188 h2mb4p No 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate C5H9O8P2 -3 C11811 KEGG C11811 JLR see PMID 12010124 317 h2o No H2O H2O 0 7732-18-5 C00001 KEGG - C00001 315 h2o2 No Hydrogen peroxide H2O2 0 7722-84-1 C00027 KEGG - C00027 Neutral Compound SMP CHS 142 h2s No Hydrogen sulfide H2S 0 6/4/7783 C00283 KEGG - C00283 Neutral Compound SMP CHS 22097 hacolipa Yes hepta-acylated core oligosaccharide lipid A (E. coli) C192H333N2O101P4 -11 AMF 22098 halipa Yes hepta-acylated KDO(2)-lipid (A) C126H226N2O40P2 -6 AMF 144 hco3 No Bicarbonate CHO3 -1 71-52-3 C00288 KEGG - C00288 SMP CHS 3844 hcys-L No L-Homocysteine C4H9NO2S 0 6027-13-0 C00155 KEGG - C00155 Deleted C05330 Neutral MF = C4H9NO2S SMP CHS Changed according to Genomatica JLR 297 hdca No Hexadecanoate (n-C16:0) C16H31O2 -1 57-10-3 C00249 "KEGG - C00249 Neutral MF = C16H32O2 SMP CHS changed official name from Fatty acid (Palmitate, n-C16:0) to hexadecanoic acid; abbreviation chagned from fa8 to hdca; changed compound class from reviewed to fatty acid - NCD C16:0" 5725 hdcea No Hexadecenoate (n-C16:1) C16H29O2 -1 "KEGG - C08362 Neutral MF = C16H30O2 SMP monounsaturated fatty acid, 16 carbons changed name from Fatty acid (n-C16:1) to hexadecenoic acid; changed abbreviation from fa7 to hdcea; changed compound class from peptides to fatty acid - NCD updated names, added KEGG entry" 8780 hdcoa Yes Hexadecenoyl-CoA (n-C16:1CoA) C37H60N7O17P3S -4 NCD C16:1 - C16H29O2 (charge -1) CoA - C21H32N7O16P3S (charge -4) NJ 3801 hdd2coa Yes trans-Hexadec-2-enoyl-CoA C37H60N7O17P3S -4 C05272 KEGG - C05272 Neutral MF = C37H64N7O17P3S SMP 1 degree of unsaturation 10496 hdeACP No cis-hexadec-9-enoyl-[acyl-carrier protein] (n-C16:1) C27H49N2O8PRS -1 "tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 5846 hemeO No Heme O C49H56FeN4O5 -2 "No KEGG Entry Neutral MF = C49H58FeN4O5 SMP Note Neidhardt picture (pg 734) is incorrect Checked N-groups, JLR" 4244 hexACP Yes Hexanoyl-ACP (n-C6:0ACP) C17H31N2O8PRS -1 8/6/7783 C05749 KEGG - C05749 AMF 460 hg2 Yes Hg2+ Hg 2 C00703 KEGG - C00703 22065 hhlipa Yes heptosyl-heptosyl-kdo2-lipidA C124H220N2O51P2 -6 AMF 11120 his-L No L-Histidine C6H9N3O2 0 71-00-1 C00135 KEGG - C00135 Neutral MF = C6H9N3O2 SMP CHS Changed according to Genomatica JLR 879 hisp No L-Histidinol phosphate C6H11N3O4P -1 25679-93-0 C01100 KEGG - C01100 Neutral MF = C6H12N3O4P SMP CHS Changed according to Genomatica JLR 11864 histd No L-Histidinol C6H12N3O 1 None C00860 KEGG - C00860 Neutral Compound SMP CHS Changed according to Genomatica JLR 7107 histrna Yes L-Histidyl-tRNA(His) C6H8N3OR 1 C02988 KEGG - C02988 SMP adjusted for Genomatica's change to aa - NCD 3953 hkndd No "2-Hydroxy-6-oxonona-2,4-diene-1,9-dioate" C9H8O6 -2 53-42-9 C04479 KEGG - C04479 Neutral-C9H10O6 JLR Changed to -2 charge 9382 hkntd No 2-hydroxy-6-ketononatrienedioate C9H6O6 -2 "No Kegg entry, see PMID: 9603882 Neutral- C9H8O6 JLR Changed to -2 charge" 22064 hlipa Yes heptosyl-kdo2-lipidA C117H208N2O45P2 -6 AMF 838 hmbil No Hydroxymethylbilane C40H38N4O17 -8 73023-76-4 C01024 KEGG - C01024 Neutral MF = C40H46N4O17 SMP CHS Checked N-groups JLR 9538 hmfurn No 4-hydroxy-5-methyl-3(2H)-furanone C5H6O3 0 No Kegg Entry See PMID: 11489131 JLR 21355 hmgth Yes hydroxymethylglutathione C11H18N3O7S -1 AMF 131 hom-L No L-Homoserine C4H9NO3 0 672-15-1 C00263 KEGG - C00263 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR 22075 hphhlipa Yes heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H231N2O60P3 -8 AMF 242 hpyr No Hydroxypyruvate C3H3O4 -1 1113-60-6 C00168 KEGG - C00168 Neutral MF = C3H4O4 SMP CHS 358 hqn No Hydroquinone C6H6O2 0 123-31-9 C00530 KEGG - C00530 SMP 3800 hx2coa Yes trans-Hex-2-enoyl-CoA C27H40N7O17P3S -4 C05271 KEGG - C05271 Neutral MF = C27H44N7O17P3S SMP 1004 hxa Yes Hexanoate (n-C6:0) C6H11O2 -1 142-62-1 C01585 KEGG - C01585 Neutral MF = C6H12O2 SMP changed compound class from peptides - NCD 218 hxan No Hypoxanthine C5H4N4O 0 68-94-0 C00262 KEGG - C00262 Neutral Compound SMP CHS Checked N-groups JLR 3799 hxcoa Yes Hexanoyl-CoA (n-C6:0CoA) C27H42N7O17P3S -4 C05270 KEGG - C05270 Neutral MF = C27H46N7O18P3S SMP 4323 iasp No Iminoaspartate C4H3NO4 -2 C05840 "KEGG - C05840 Neutral MF = C4H5NO4 SMP Checked N-groups, agrees with ACD software, JLR Updated after checking with Pipeline Pilot, RM ==> C4H3NO4 -2" 740 ichor No Isochorismate C10H8O6 -2 C00885 KEGG - C00885 Neutral MF = C10H10O6 SMP CHS 158 icit No Isocitrate C6H5O7 -3 30810-51-6 C00311 KEGG - C00311 Neutral MF = C6H8O7 SMP CHS 22072 icolipa Yes inner core oligosaccharide lipid A (E coli) C145H251N2O74P4 -11 AMF 11158 idon-L No L-Idonate C6H11O7 -1 1114-17-6 C00770 KEGG - C00770 Neutral-C6H12O7 JLR 1067 idp No IDP C10H11N4O11P2 -3 86-04-4 C00104 KEGG - C00104 Neutral MF = C10H14N4O11P2 SMP CHS Checked N-groups JLR 410 ile-L No L-Isoleucine C6H13NO2 0 73-32-5 C00407 KEGG - C00407 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR 7110 iletrna Yes L-Isoleucyl-tRNA(Ile) C6H12NOR 1 C03127 KEGG - C03127 SMP adjusted for Genomatica's change to aa - NCD 7138 imacp No 3-(Imidazol-4-yl)-2-oxopropyl phosphate C6H7N2O5P -2 C01267 KEGG - C01267 Neutral MF = C6H9N2O5P SMP CHS Checked N-groups JLR 1090 imp No IMP C10H11N4O8P -2 131-99-7 C00130 KEGG - C00130 Neutral MF = C10H13N4O8P SMP CHS Checked N-groups JLR 82 indole No Indole C8H7N 0 120-72-9 C00463 KEGG - C00463 Checked N-groups JLR 223 inost No myo-Inositol C6H12O6 0 87-89-8 C00137 KEGG - C00137 Neutral Compound SMP CHS 147 ins No Inosine C10H12N4O5 0 58-63-9 C00294 KEGG - C00294 Neutral Compound SMP CHS Checked N-groups JLR 1089 ipdp No Isopentenyl diphosphate C5H9O7P2 -3 C00129 KEGG - C00129 Neutral MF = C5H12O7P2 SMP 3701 isetac Yes Isethionic acid C2H5O4S -1 107-36-8 C05123 KEGG - C05123 SAB charged following taurine's charge 1050 itp No ITP C10H11N4O14P3 -4 132-06-9 C00081 KEGG - C00081 Neutral MF = C10H15N4O14P3 SMP CHS Checked N-groups JLR 289 k No potassium K 1 C00238 KEGG - C00238 778 kdo No 3-Deoxy-D-manno-2-octulosonate C8H13O8 -1 C01187 KEGG - C01187 Neutral MF = C8H14O8 SMP CHS 8360 kdo2lipid4 No KDO(2)-lipid IV(A) C84H148N2O37P2 -6 C06025 KEGG C06025 Neutral C84H154N2O37P2 JLR - NH page 1043 8361 kdo2lipid4L No KDO(2)-lipid IV(A) with laurate C96H170N2O38P2 -6 C06251 C06251 NH page 1043 Neutral-C96H176N2O38P2 JLR 11297 kdo2lipid4p No KDO(2)-lipid IV(A) with palmitoleoyl C100H176N2O38P2 -6 see PMID 10092655 Neutral-C100H182N2O38P2 JLR 3952 kdo8p No 3-Deoxy-D-manno-octulosonate 8-phosphate C8H12O11P -3 C04478 KEGG - C04478 Neutral MF = C8H15O11P SMP CHS 8745 kdolipid4 No KDO-lipid IV(A) C76H137N2O30P2 -5 C06024 KEGG- C06024 Neutral C76H142N2O30P2 JLR- 22077 kphphhlipa Yes kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C139H241N2O70P4 -11 AMF 304 lac-D No D-Lactate C3H5O3 -1 10326-41-7 C00256 KEGG - C00256 Neutral MF = C3H6O3 SMP CHS 10931 lac-L No L-Lactate C3H5O3 -1 79-33-4 C00186 KEGG - C00186 Neutral MF = C3H6O3 SMP CHS 21424 LalaDglu Yes L-alanine-D-glutamate C8H13N2O5 -1 AMF 21425 LalaDgluMdap Yes "L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate" C15H25N4O8 -1 AMF 21426 LalaDgluMdapDala Yes "L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine" C18H30N5O9 -1 AMF 21556 LalaLglu Yes L-alanine-L-glutamate C8H13N2O5 -1 AMF dont think its the same as gluala 491 lald-D Yes D-Lactaldehyde C3H6O2 0 None C00937 KEGG - C00937 Neutral Compound SMP CHS 420 lald-L No L-Lactaldehyde C3H6O2 0 598-35-6 C00424 KEGG - C00424 Neutral Compound SMP CHS 292 lcts No Lactose C12H22O11 0 63-42-3 C00243 KEGG - C00243 Neutral Compound SMP CHS 1082 leu-L No L-Leucine C6H13NO2 0 61-90-5 C00123 KEGG - C00123 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR 7098 leutrna Yes L-Leucyl-tRNA(Leu) C6H12NOR 1 C02047 KEGG -C02047 SMP adjusted for Genomatica's change to aa - NCD 2477 lgt-S No (R)-S-Lactoylglutathione C13H20N3O8S -1 59-85-8 C03451 KEGG - C03451 Neutral MF = C13H21N3O8S SMP CHS Changed according to Genomatica JLR 4466 lipa No KDO(2)-lipid (A) C110H196N2O39P2 -6 598-35-6 C06026 KEGG - C06026 NH page 1043 JLR 9012 lipa_cold No cold adapted KDO(2)-lipid (A) C114H202N2O39P2 -6 see PMID 10092655 Neutral C114H208N2O39P2 JLR 3637 lipidA No "2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate" C68H126N2O23P2 -4 None Neutral MF = C68H130N2O23P2 SMP CHS JLR- similar to C04919 but phosphate is on a different oxygen(see NH pg 1043). Changed to -4 charge 5873 lipidAds No Lipid A Disaccharide C68H127N2O20P -2 C04932 tv Kegg C04932 3555 lipidX No "2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate" C34H64NO12P -2 None C04824 KEGG - C04824 Neutral MF = C34H66NO12P SMP CHS Checked N-groups JLR 26364 lpp Yes lipoprotein XC16H30O1 0 6244-92-4 C01834 KEGG - C01834 AMF lipoprotein that has been N-acylated 328 lys-L No L-Lysine C6H15N2O2 1 56-87-1 C00047 KEGG - C00047 Neutral MF = C6H14N2O2 SMP CHS Changed according to Genomatica JLR 5855 lystrna Yes L-Lysine-tRNA (Lys) C6H14N2OR 2 C01931 KEGG - C01931 SMP adjusted for Genomatica's change to aa - NCD 1236 lyx-L Yes L-Lyxose C5H10O5 0 1949-78-6 C01508 KEGG - C01508 JLR 50 malACP No Malonyl-[acyl-carrier protein] C14H22N2O10PRS -2 None C01209 "KEGG - C01209 Error in KEGG: ACP attached to Malonyl via a S, NOT Oxygen. Checked with Neidhardt (tv) Neutral MF = C3H3O3R (S)R = [acyl-carrier protein] SMP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) " 11267 malcoa No Malonyl-CoA C24H33N7O19P3S -5 524-14-1 C00083 KEGG - C00083 Neutral MF = C24H38N7O19P3S SMP CHS 230 mal-L No L-Malate C4H4O5 -2 97-67-6 C00149 KEGG - C00149 Neutral MF = C4H6O5 SMP CHS 267 malt No Maltose C12H22O11 0 69-79-4 C00208 KEGG - C00208 Neutral Compound SMP CHS 2247 malt6p No Maltose 6'-phosphate C12H21O14P -2 None C02995 KEGG - C02995 Neutral MF = C12H23O14P SMP CHS 9036 malthp No Maltoheptaose C42H72O36 0 Not in Kegg JLR 1564 malthx No Maltohexaose C36H62O31 0 34620-77-4 C01936 KEGG - C01936 JLR 9035 maltpt No Maltopentaose C30H52O26 0 Not in Kegg JLR 1284 malttr No Maltotriose C18H32O16 0 1109-28-0 C01835 KEGG - C01835 JLR 1658 maltttr No Maltotetraose C24H42O21 0 34612-38-9 C02052 KEGG - C02052 JLR 11018 man Yes D-Mannose C6H12O6 0 3458-28-4 C00159 KEGG - C00159 Neutral Compound SMP CHS 2920 man1p No D-Mannose 1-phosphate C6H11O9P -2 C03812 KEGG - C03812 Neutral MF = C6H13O9P SMP CHS 137 man6p No D-Mannose 6-phosphate C6H11O9P -2 None C00275 KEGG - C00275 Neutral MF = C6H13O9P SMP CHS 12435 man6pglyc Yes 2(alpha-D-Mannosyl-6-phosphate)-D-glycerate C9H14O12P -3 JLR- not in Kegg The same as manglyc but with a phosphate group on the 6th carbon of the mannose moiety 128 mana No D-Mannonate C6H11O7 -1 C00514 KEGG - C00514 Neutral MF = C6H12O7 SMP 12434 manglyc Yes 2(alpha-D-Mannosyl)-D-glycerate C9H15O9 -1 C11544 KEGG C11544 3898 melib No Melibiose C12H22O11 0 585-99-9 C05402 KEGG - C05402 Neutral compound CAS # covers alpha-D-(+)-Melibiose hydrate SMP CHS 794 mercppyr Yes Mercaptopyruvate C3H3O3S -1 C00957 KEGG - C00957 723 met-D No D-Methionine C5H10NO2S 0 348-67-4 C00855 KEGG - C00855 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR 433 methf No "5,10-Methenyltetrahydrofolate" C20H20N7O6 -1 C00445 "KEGG - C00445 Merged with C04270 Neutral MF = C20H22N7O6 netural form has +1 charge -NCD SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR Agrees with pipeline pilot" 343 met-L No L-Methionine C5H11NO2S 0 63-68-3 C00073 KEGG - C00073 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR 18416 metsox-R-L Yes L-methionine-R-sulfoxide C5H11NO3S 0 "MKA KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR " 10541 metsox-S-L Yes L-Methionine-S-Sulfoxide C5H11NO3S 0 C02989 "KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR Kegg C02989" 5854 mettrna Yes L-Methionyl-tRNA (Met) C5H10NOSR 1 C02430 KEGG - C02430 SMP adjusted for Genomatica's change to aa - NCD 12857 mg2 Yes magnesium Mg 2 C00305 KEGG - C00305 SMP 8983 mi1p-D No 1D-myo-Inositol 1-phosphate C6H11O9P -2 C01177 Kegg C01177 Neutral-C6H13O9P JLR 3284 micit No methylisocitrate C7H7O7 -3 20298-95-7 C04593 KEGG - C04593 Neutral-C7H10O7 JLR 938 minohp Yes myo-Inositol hexakisphosphate C6H6O24P6 -12 C01204 KEGG - C01204 JLR 11043 mlthf No "5,10-Methylenetetrahydrofolate" C20H21N7O6 -2 C00143 "KEGG - C00143 Neutral MF = C20H23N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR" 943 mmcoa-R No (R)-Methylmalonyl-CoA C25H35N7O19P3S -5 C01213 KEGG - C01213 Neutral MF = C25H40N7O19P3S SMP Checked N-groups JLR 451 mmcoa-S No (S)-Methylmalonyl-CoA C25H35N7O19P3S -5 C00683 KEGG - C00683 Neutral MF = C25H40N7O19P3S SMP CHS Checked N-groups JLR 2185 mmet Yes S-Methyl-L-methionine C6H14NO2S 1 4289-98-9 C03172 "KEGG - C03172 NCD changed to protonated form, added charge - NCD" 320 mn2 Yes Mn2+ Mn 2 None C00034 KEGG - C00034 SMP CHS 400 mnl Yes D-Mannitol C6H14O6 0 69-65-8 C00392 KEGG - C00392 SMP 1128 mnl1p No D-Mannitol 1-phosphate C6H13O9P -2 C00644 KEGG - C00644 Neutral MF = C6H15O9P SMP 4630 mobd Yes Molybdate MoO4 -2 C06232 KEGG - C06232 Neutral MF = H2MoO4 SMP 4306 mql8 No Menaquinol 8 C51H74O2 0 C05819 KEGG - C05819 General Formula = C16H18O2(C5H8)n; n = 7 for mql7 SMP 9 mqn8 No Menaquinone 8 C51H72O2 0 84-81-1 C00828 KEGG - C00828 General Formula = C16H16O2(C5H8)n; n = 7 for mqn8; See also mq SMP CHS 21348 mso3 Yes methanesulfonate CH3O3S -1 0 370 mthgxl No Methylglyoxal C3H4O2 0 78-98-8 C00546 KEGG - C00546 Neutral Compound SMP CHS 25720 murein3p3p Yes "two linked disacharide tripeptide murein units (uncrosslinked, middle of chain)" C68H104N12O38 -4 AMF PMID: 9751644 has a good figure 25725 murein3px3p Yes "two disacharide linked murein units, tripeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)" C68H102N12O37 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->A2pm 25718 murein3px4p Yes "two disacharide linked murein units, tripeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)" C71H107N13O38 -4 AMF PMID: 9751644 has a good figure 25793 murein4p3p Yes "two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain)" C71H109N13O39 -4 AMF PMID: 9751644 has a good figure 25719 murein4p4p Yes "two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)" C74H114N14O40 -4 AMF PMID: 9751644 has a good figure 25717 murein4px4p Yes "two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)" C74H112N14O39 -4 AMF PMID: 9751644 has a good figure 25839 murein4px4p4p Yes "three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala), one uncrosslinked tetrapaptide) (middle of chain)" C111H169N21O59 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala 25723 murein4px4px4p Yes three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) C111H167N21O58 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala 25794 murein5p3p Yes "two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain)" C74H114N14O40 -4 AMF PMID: 9751644 has a good figure 25792 murein5p4p Yes "two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain)" C77H119N15O41 -4 AMF PMID: 9751644 has a good figure 21438 murein5p5p Yes "two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)" C80H124N16O42 -4 "AMF this is formed when two uaagmda units come together and lose their undecprenyl chains [GlcNac-MurNac-pentapeptide(beta1->4)GlcNac-MurNac-pentapeptide] unit only the leading oxygen from the ether bond to the next unit is kept on the MurNac, the one from the previous unit connected to the terminal GlcNac is not considered PMID: 9751644 has a good figure" 25721 murein5p5p5p Yes "three linked disacharide pentapeptide murein units (uncrosslinked, middle of chain)" C120H186N24O63 -6 AMF 25724 murein5px3p Yes "two disacharide linked murein units, pentapeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain)" C74H112N14O39 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->A2pm 25716 murein5px4p Yes "two disacharide linked murein units, pentapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)" C77H117N15O40 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->D-ala 25722 murein5px4px4p Yes three disacharide linked murein units (pentapeptide corsslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) C114H172N22O59 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala 10495 myrsACP No Myristoyl-ACP (n-C14:0ACP) C25H47N2O8PRS -1 C05761 "KEGG C05761 tv myrs component = C14H27O (3/25/03) JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 1108 N1aspmd No N1-Acetylspermidine C9H23N3O 2 34450-16-3 C00612 KEGG - C00612 JLR capitalized N at beginning of abbrev -NCD Checked N-groups JLR 10910 n2o Yes Nitrous oxide N2O 0 10024-97-2 C00887 KEGG - C00887 SMP CHS 842 n8aspmd No N8-Acetylspermidine C9H23N3O 2 34450-15-2 C01029 KEGG - C01029 JLR Checked N-groups JLR 1023 na1 No Sodium Na 1 7440-23-5 C01330 KEGG - C01330 SMP CHS 301 nac No Nicotinate C6H4NO2 -1 59-67-6 C00253 KEGG - C00253 Neutral MF = C6H5NO2 SMP CHS Checked N-groups JLR 466 nad No Nicotinamide adenine dinucleotide C21H26N7O14P2 -1 53-84-9 C00003 KEGG - C00003 Neutral MF = C21H28N7O14P2 (Charge +1) SMP CHS Checked N-groups JLR (agrees with ACD software) 467 nadh No Nicotinamide adenine dinucleotide - reduced C21H27N7O14P2 -2 53-84-9 C00004 "KEGG - C00004 Neutral MF = C21H29N7O14P2 SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR" 469 nadp No Nicotinamide adenine dinucleotide phosphate C21H25N7O17P3 -3 53-59-8 C00006 KEGG - C00006 Original KEGG MF = C21H29N7O17P3 (+1) SMP CHS Checked N-groups JLR 468 nadph No Nicotinamide adenine dinucleotide phosphate - reduced C21H26N7O17P3 -4 2646-71-1 C00005 "KEGG - C00005 Neutral MF = C21H30N7O17P3 SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR" 233 ncam No Nicotinamide C6H6N2O 0 98-92-0 C00153 KEGG - C00153 SMP CHS Checked N-groups JLR 476 nh4 No Ammonium H4N 1 66701-25-5 C01342 KEGG - C01342 Charged Compound Diiferentiate Ammonia from Ammonium SMP CHS Checked N-groups JLR 10781 ni2 Yes nickel Ni 2 C00291 KEGG - C00291 776 nicrnt No Nicotinate D-ribonucleotide C11H12NO9P -2 C01185 KEGG - C01185 Neutral MF = C11H15NO9P SMP Checked N-groups JLR 77 nmn No NMN C11H14N2O8P -1 1094-61-7 C00455 KEGG - C00455 Correct MF = C11H16N2O8P KEGG MF = C11H15N2O8P with charge +1 SMP Checked N-groups JLR 2239 Nmtrp Yes N-Methyltryptophan C12H14N2O2 0 526-31-8 C02983 KEGG - C02983 361 no Yes Nitric oxide NO 0 10102-43-9 C00533 KEGG - C00533 SMP CHS 11261 no2 No Nitrite NO2 -1 7697-37-2 C00088 KEGG - C00088 Neutral MF = HNO2 SMP CHS Checked N-groups JLR 5270 no3 No Nitrate NO3 -1 C00244 KEGG - C00244 Neutral MF = HNO3 SMP CHS Checked N-goups JLR 22132 o16a2und Yes (O16 antigen)x2 undecaprenyl diphosphate C123H200N2O57P2 -2 AMF 22133 o16a3und Yes (O16 antigen)x3 undecaprenyl diphosphate C157H255N3O82P2 -2 AMF 22135 o16a4colipa Yes (O16 antigen)x4 core oligosaccharide lipid A C312H523N6O200P4 -11 AMF 22134 o16a4und Yes (O16 antigen)x4 undecaprenyl diphosphate C191H310N4O107P2 -2 AMF 22131 o16aund Yes O16 antigen undecaprenyl diphosphate C89H145N1O32P2 -2 AMF - structure from PMID: 7517391 470 o2 No O2 O2 0 7782-44-7 C00007 KEGG - C00007 SMP CHS 461 o2- No Superoxide anion O2 -1 C00704 KEGG - C00704 JLR 322 oaa No Oxaloacetate C4H2O5 -2 328-42-7 C00036 KEGG - C00036 Neutral MF = C4H4O5 SMP CHS 3805 oc2coa Yes trans-Oct-2-enoyl-CoA C29H44N7O17P3S -4 C05276 KEGG - C05276 Neutral MF = C29H48N7O18P3S SMP 7928 ocACP Yes Octanoyl-ACP (n-C8:0ACP) C19H35N2O8PRS -1 C05752 "JLR- saturated fatty acid with 8 carbons attached to ACP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 10688 occoa Yes Octanoyl-CoA (n-C8:0CoA) C29H46N7O17P3S -4 C01944 KEGG - C01944 Neutral MF = C29H50N7O17P3S SMP 1249 ocdca No octadecanoate (n-C18:0) C18H35O2 -1 57-11-4 C01530 "KEGG - C01530 Neutral MF = C18H36O2 SID: 38708 CID: 78387 SMP saturated fatty acid, 18 carbons changed compound class from peptides to fatty acids - NCD" 5936 ocdcaACP Yes Octadecanoyl-ACP (n-C18:0ACP) C29H55N2O8PRS -1 "tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS)" 8769 ocdcea No octadecenoate (n-C18:1) C18H33O2 -1 "monounsaturated fatty acid, 18 carbons KEGG - C00712 NCD updated by NJ" 5354 octa Yes octanoate (n-C8:0) C8H15O2 -1 124-07-2 C06423 KEGG - C06423 Neutral MF = C8H16O2 SMP changed compound class from peptides - NCD 2970 octdp No all-trans-Octaprenyl diphosphate C40H65O7P2 -3 C04146 KEGG - C04146 Neutral MF = C40H68O7P2 SMP 5871 octeACP No cis-octadec-11-enoyl-[acyl-carrier protein] (n-C18:1) C29H53N2O8PRS -1 "tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 8401 od2coa Yes trans-Octadec-2-enoyl-CoA C39H64N7O17P3S -4 NCD C18:1 - C18H33O2 (charge -1) C21H32N7O16P3S (charge -4) NJ 8782 odecoa Yes Octadecenoyl-CoA (n-C18:1CoA) C39H64N7O17P3S -4 NCD KEGG - C00510 C18:1 C18H33O2 (charge -1) CoA - C21H32N7O16P3S charge (-4) NJ 8083 ohpb No 2-Oxo-3-hydroxy-4-phosphobutanoate C4H4O8P -3 C06054 KEGG - C06054 Neutral-C4H7O8P JLR 1097 op4en No 2-Oxopent-4-enoate C5H5O3 -1 C00596 KEGG - C00596 Neutral-C5H6O3 JLR 1304 orn No Ornithine C5H13N2O2 1 70-26-8 C01602 KEGG - C01602 Neutral MF = C5H12N2O2 SMP CHS Checked N-groups JLR 148 orot No Orotate C5H3N2O4 -1 65-86-1 C00295 KEGG - C00295 Neutral MF = C5H4N2O4 SMP CHS Checked N-groups JLR 881 orot5p No Orotidine 5'-phosphate C10H10N2O11P -3 2149-82-8 C01103 KEGG - C01103 Neutral MF = C10H13N2O11P SMP Checked N-groups JLR 580 oxam Yes Oxamate C2H2NO3 -1 471-47-6 C01444 KEGG - C01444 JLR- Checked protonation state 651 oxur Yes Oxalureate C3H3N2O4 -1 585-05-7 C00802 KEGG - C00802 Checked Protonation state JLR 26133 pa120 Yes "1,2-didodecanoyl-sn-glycerol 3-phosphate" C27H51O8P1 -2 C00416 KEGG - C00416 AMF 26056 pa140 Yes "1,2-ditetradecanoyl-sn-glycerol 3-phosphate" C31H59O8P1 -2 C00416 AMF 26059 pa141 Yes "1,2-ditetradec-7-enoyl-sn-glycerol 3-phosphate" C31H55O8P1 -2 C00416 AMF 26057 pa160 Yes "1,2-dihexadecanoyl-sn-glycerol 3-phosphate" C35H67O8P1 -2 C00416 AMF 26060 pa161 Yes "1,2-dihexadec-9-enoyl-sn-glycerol 3-phosphate" C35H63O8P1 -2 C00416 AMF 26058 pa180 Yes "1,2-dioctadecanoyl-sn-glycerol 3-phosphate" C39H75O8P1 -2 C00416 AMF 26061 pa181 Yes "1,2-dioctadec-11-enoyl-sn-glycerol 3-phosphate" C39H71O8P1 -2 C00416 AMF 9657 pac No Phenylacetic acid C8H7O2 -1 CAS: 103-82-2 C07086 Kegg C07086 Neutral-C8H8O2 JLR 1100 pacald No Phenylacetaldehyde C8H8O 0 122-78-1 C00601 KEGG - C00601 JLR 5870 palmACP No Palmitoyl-ACP (n-C16:0ACP) C27H51N2O8PRS -1 C05764 "KEGG- C05764 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 900 pan4p No Pantetheine 4'-phosphate C11H21N2O7PS -2 C01134 KEGG - C01134 Neutral MF = C11H23N2O7PS SMP CHS Checked N-groups JLR 351 pant-R No (R)-Pantoate C6H11O4 -1 470-29-1 C00522 KEGG - C00522 Neutral MF = C6H12O4 SMP CHS 333 pap No "Adenosine 3',5'-bisphosphate" C10H11N5O10P2 -4 1053-73-2 C00054 KEGG - C00054 Neutral MF = C10H15N5O10P2 SMP CHS 332 paps No 3'-Phosphoadenylyl sulfate C10H11N5O13P2S -4 482-67-7 C00053 KEGG - C00053 Neutral MF = C10H15N5O13P2S SMP Checked N-groups JLR 1116 pdx5p No Pyridoxine 5'-phosphate C8H10NO6P -2 447-05-2 C00627 KEGG - C00627 Neutral MF = C8H12NO6P SMP CHS Checked N-groups JLR 26139 pe120 Yes "phosphatidylethanolamine (didodecanoyl, n-C12:0)" C29H58N1O8P1 0 C00350 KEGG - C00350 AMF 26100 pe140 Yes "phosphatidylethanolamine (ditetradecanoyl, n-C14:0)" C33H66N1O8P1 0 C00350 KEGG - C00350 AMF 26103 pe141 Yes "phosphatidylethanolamine (ditetradec-7-enoyl, n-C14:1)" C33H62N1O8P1 0 C00350 KEGG - C00350 AMF 26101 pe160 Yes "phosphatidylethanolamine (dihexadecanoyl, n-C16:0)" C37H74N1O8P1 0 C00350 KEGG - C00350 AMF 26104 pe161 Yes "phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)" C37H70N1O8P1 0 C00350 KEGG - C00350 AMF 26102 pe180 Yes "phosphatidylethanolamine (dioctadecanoyl, n-C18:0)" C41H82N1O8P1 0 C00350 KEGG - C00350 AMF 26105 pe181 Yes "phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1)" C41H78N1O8P1 0 C00350 KEGG - C00350 AMF 9637 peamn No Phenethylamine C8H12N 1 64-04-0 C05332 KEGG - C05332 JLR Checked N-groups JLR 344 pep No Phosphoenolpyruvate C3H2O6P -3 138-08-9 C00074 KEGG - C00074 Neutral MF = C3H5O6P SMP CHS 26136 pg120 Yes "Phosphatidylglycerol (didodecanoyl, n-C12:0)" C30H58O10P1 -1 C00344 KEGG - C00344 AMF 26083 pg140 Yes "Phosphatidylglycerol (ditetradecanoyl, n-C14:0)" C34H66O10P1 -1 C00344 KEGG - C00344 AMF 26086 pg141 Yes "Phosphatidylglycerol (ditetradec-7-enoyl, n-C14:1)" C34H62O10P1 -1 C00344 KEGG - C00344 AMF 26084 pg160 Yes "Phosphatidylglycerol (dihexadecanoyl, n-C16:0)" C38H74O10P1 -1 C00344 KEGG - C00344 AMF 26087 pg161 Yes "Phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1)" C38H70O10P1 -1 C00344 KEGG - C00344 AMF 26085 pg180 Yes "Phosphatidylglycerol (dioctadecanoyl, n-C18:0)" C42H82O10P1 -1 C00344 KEGG - C00344 AMF 26088 pg181 Yes "Phosphatidylglycerol (dioctadec-11-enoyl, n-C18:1)" C42H78O10P1 -1 C00344 KEGG - C00344 AMF 26135 pgp120 Yes "Phosphatidylglycerophosphate (didodecanoyl, n-C12:0)" C30H57O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 2979 pgp140 Yes "Phosphatidylglycerophosphate (ditetradecanoyl, n-C14:0)" C34H65O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 26080 pgp141 Yes "Phosphatidylglycerophosphate (ditetradec-7-enoyl, n-C14:1)" C34H61O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 26078 pgp160 Yes "Phosphatidylglycerophosphate (dihexadecanoyl, n-C16:0)" C38H73O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 26081 pgp161 Yes "Phosphatidylglycerophosphate (dihexadec-9-enoyl, n-C16:1)" C38H69O13P2 -3 94-62-2 KEGG - C03892 AMF 26079 pgp180 Yes "Phosphatidylglycerophosphate (dioctadecanoyl, n-C18:0)" C42H81O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 26082 pgp181 Yes "Phosphatidylglycerophosphate (dioctadec-11-enoyl, n-C18:1)" C42H77O13P2 -3 94-62-2 C03892 KEGG - C03892 AMF 397 phaccoa No Phenylacetyl-CoA C29H38N7O17P3S -4 C00582 KEGG - C00582 Neutral-C29H42N7O17P3S JLR 1048 phe-L No L-Phenylalanine C9H11NO2 0 63-91-2 C00079 KEGG - C00079 Neutral MF = C9H11NO2 SMP CHS Changed according to Genomatica JLR 11520 pheme No Protoheme C34H30FeN4O4 -2 14875-96-8 C00032 "KEGG - C00032 Neutral MF = C34H32FeN4O4 Note that chemfinder has the incorrect formula SMP CHS Checked N-groups, JLR" 7112 phetrna Yes L-Phenylalanyl-tRNA(Phe) C9H10NOR 1 C03511 KEGG - C03511 SMP adjusted for Genomatica's change to aa - NCD 22073 phhlipa Yes phospho-heptosyl-heptosyl-kdo2-lipidA C124H219N2O54P3 -8 AMF 10564 phom No O-Phospho-L-homoserine C4H8NO6P -2 C01102 KEGG - C01102 Neutral MF = C4H10NO6P SMP CHS Changed according to Genomatica JLR 22076 phphhlipa Yes phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H230N2O63P4 -10 AMF 240 phpyr No Phenylpyruvate C9H7O3 -1 156-06-9 C00166 KEGG - C00166 Neutral MF = C9H8O3 SMP CHS 8887 phthr No O-Phospho-4-hydroxy-L-threonine C4H8NO7P -2 C06055 KEGG - C06055 NCD Checked N-groups JLR 472 pi No Phosphate HO4P -2 14265-44-2 C00009 KEGG - C00009 Neutral MF = H3O4P SMP CHS Formula changed to HPO4 (Charge -2) on Feb-26-2002 696 pmcoa No Pimeloyl-CoA C28H41N7O19P3S -5 C01063 KEGG - C01063 Neutral MF = C28H46N7O19P3S SMP CHS 11029 pmtcoa Yes Palmitoyl-CoA (n-C16:0CoA) C37H62N7O17P3S -4 C00154 KEGG - C00154 Neutral MF = C37H66N7O17P3S SMP changed compound class from peptides to fatty acids - NCD C16:0 - C16H31O2 (charge -1) CoA - C21H32N7O16P3S (charge -4) NJ 10928 pnto-R No (R)-Pantothenate C9H16NO5 -1 79-83-4 C00864 Deleted KEGG - C00864 KEGG - C02349 Neutral MF = C9H17NO5 SMP CHS Checked N-groups JLR 238 ppa No Propionate (n-C3:0) C3H5O2 -1 79-09-4 C00163 KEGG - C00163 Neutral MF = C3H6O2 SMP NCD 96 ppal Yes Propanal C3H6O 0 123-38-6 C00479 KEGG - C00479 Neutral Compound SMP 2157 ppap No Propanoyl phosphate C3H5O5P -2 121-69-7 C02876 KEGG - C02876 Neutral: C3H7O5P JLR 487 ppbng No Porphobilinogen C10H13N2O4 -1 487-90-1 C00931 KEGG - C00931 Neutral MF = C10H14N2O4 SMP Changed according to Genomatica JLR 1064 ppcoa No Propanoyl-CoA C24H36N7O17P3S -4 317-66-8 C00100 KEGG - C00100 Neutral MF = C24H40N7O17P3S SMP CHS NCD 957 ppgpp Yes "Guanosine 3',5'-bis(diphosphate)" C10H11N5O17P4 -6 C01228 KEGG - C01228 Neutral MF = C10H17N5O17P4 SMP 302 pphn No Prephenate C10H8O6 -2 126-49-8 C00254 KEGG - C00254 Neutral MF = C10H10O6 SMP CHS 475 ppi No Diphosphate HO7P2 -3 9/3/2466 C00013 KEGG - C00013 Neutral MF = H4O7P2 SMP CHS Formula changed to HO7P2 (Charge -3) on Feb-26-2002 1772 ppp9 No Protoporphyrin C34H32N4O4 -2 553-12-8 C02191 KEGG - C02191 Neutral MF = C34H34N4O4 SMP CHS 864 pppg9 No Protoporphyrinogen IX C34H38N4O4 -2 C01079 KEGG - C01079 Neutral MF = C34H40N4O4 SMP Checked N-groups JLR 2452 pppi No Inorganic triphosphate HO10P3 -4 C03279 KEGG - C03279 Neutral MF = H5O10P3 SMP 4152 pppn No Phenylpropanoate C9H9O2 -1 2628-17-3 C05629 KEGG - C05629 Neutral-C9H10O2 JLR 4912 ppt Yes Phosphonate HO3P -2 13598-36-2 C06701 KEGG - C06701 JLR Pka- 2 and 6.58 (http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf) 2325 pram No 5-Phospho-beta-D-ribosylamine C5H11NO7P -1 C03090 KEGG - C03090 Neutral MF = C5H12NO7P SMP CHS Changed according to Genomatica JLR 9634 pran No N-(5-Phospho-D-ribosyl)anthranilate C12H13NO9P -3 None C04302 KEGG - C04302 Neutral MF = C12H16NO9P SMP CHS Checked N-groups JLR 2778 prbamp No 1-(5-Phosphoribosyl)-AMP C15H19N5O14P2 -4 C02741 KEGG - C02741 Neutral MF = C15H23N5O14P2 SMP CHS 2058 prbatp No 1-(5-Phosphoribosyl)-ATP C15H19N5O20P4 -6 C02739 KEGG - C02739 Neutral MF = C15H25N5O20P4 SMP CHS 3612 prfp No 1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide C15H21N5O15P2 -4 C04896 "KEGG - C04896 Neutral MF = C15H25N5O15P2 SMP CHS Checked N-groups, agrees with ACD software, JLR" 10680 prlp No 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide C15H21N5O15P2 -4 C04916 "KEGG - C04916 Neutral MF = C15H25N5O15P2 SMP CHS Checked N-groups, agrees with ACD software, JLR" 26302 progly Yes L-Prolinylglycine C7H12N2O3 0 AMF 229 pro-L No L-Proline C5H9NO2 0 147-85-3 C00148 KEGG - C00148 Neutral MF = C5H9NO2 SMP CHS Changed according to Genomatica JLR 7104 protrna Yes L-Prolyl-tRNA(Pro) C5H8NOR 1 C02702 KEGG - C02702 SMP adjusted for Genomatica's change to aa - NCD 1078 prpp No 5-Phospho-alpha-D-ribose 1-diphosphate C5H8O14P3 -5 C00119 KEGG - C00119 Neutral MF = C5H13O14P3 SMP 26138 ps120 Yes "phosphatidylserine (didodecanoyl, n-C12:0)" C30H57N1O10P1 -1 C02737 KEGG - C02737 AMF 26094 ps140 Yes "phosphatidylserine (ditetradecanoyl, n-C14:0)" C34H65N1O10P1 -1 C02737 KEGG - C02737 AMF 26097 ps141 Yes "phosphatidylserine (ditetradec-7-enoyl, n-C14:1)" C34H61N1O10P1 -1 C02737 KEGG - C02737 AMF 26095 ps160 Yes "phosphatidylserine (dihexadecanoyl, n-C16:0)" C38H73N1O10P1 -1 C02737 KEGG - C02737 AMF 26098 ps161 Yes "phosphatidylserine (dihexadec-9-enoyl, n-C16:1)" C38H69N1O10P1 -1 C02737 KEGG - C02737 AMF 26096 ps180 Yes "phosphatidylserine (dioctadecanoyl, n-C18:0)" C42H81N1O10P1 -1 C02737 KEGG - C02737 AMF 26099 ps181 Yes "phosphatidylserine (dioctadec-11-enoyl, n-C18:1)" C42H77N1O10P1 -1 C02737 KEGG - C02737 AMF 824 pser-L No O-Phospho-L-serine C3H6NO6P -2 407-41-0 C01005 KEGG - C01005 Neutral MF = C3H8NO6P SMP Changed according to Genomatica JLR 1094 ptrc No Putrescine C4H14N2 2 110-60-1 C00134 KEGG - C00134 Neutral Compound SMP CHS Changed according to Genomatica JLR 1130 pyam5p No Pyridoxamine 5'-phosphate C8H12N2O5P -1 529-96-4 C00647 "KEGG - C00647 Neutral MF = C8H13N2O5P SMP CHS Checked N-groups JLR, AMF " 362 pydam No Pyridoxamine C8H13N2O2 1 85-87-0 C00534 "KEGG - C00534 Neutral Compound SMP CHS Checked N-groups JLR, AMF" 298 pydx No Pyridoxal C8H9NO3 0 66-72-8 C00250 KEGG - C00250 Neutral Compound SMP CHS Checked N-groups JLR 479 pydx5p No Pyridoxal 5'-phosphate C8H8NO6P -2 54-47-7 C00018 "KEGG - C00018 Neutral MF = C8H10NO6P SMP CHS Checked N-groups JLR, AMF " 160 pydxn No Pyridoxine C8H11NO3 0 65-23-6 C00314 KEGG - C00314 Neutral Compound SMP CHS Checked N-groups JLR 311 pyr No Pyruvate C3H3O3 -1 127-17-3 C00022 KEGG - C00022 Neutral MF = C3H4O3 SMP CHS 6324 q8 No Ubiquinone-8 C49H74O4 0 1339-63-5 C00399 "KEGG C00399 Formula- C14H18O4(C5H8)n , where n=7 for q8 JLR" 6325 q8h2 No Ubiquinol-8 C49H76O4 0 C00390 KEGG C00390 JLR 2854 quln No Quinolinate C7H3NO4 -2 89-00-9 C03722 KEGG - C03722 Neutral MF = C7H5NO4 SMP CHS Checked N-groups JLR 909 r15bp Yes "D-Ribose 1,5-bisphosphate" C5H8O11P2 -4 None C01151 KEGG - C01151 Neutral MF = C5H12O11P2 SMP CHS 10390 r1p No alpha-D-Ribose 1-phosphate C5H9O8P -2 58459-37-3 C00442 KEGG - C00442 Neutral MF = C5H11O8P SMP CHS 1999 r5p No alpha-D-Ribose 5-phosphate C5H9O8P -2 4300-28-1 C00117 KEGG - C00117 Delete KEGG - C03736 Neutral MF = C5H11O8P SMP CHS 22127 ragund Yes rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C69H113N1O16P2 -2 AMF 825 rbflvrd Yes Reduced riboflavin C17H22N4O6 0 C01007 KEGG - C01007 122 rbl-L No L-Ribulose C5H10O5 0 488-84-6 C00508 KEGG - C00508 Neutral Compound SMP CHS 91 rbt Yes Ribitol C5H12O5 0 488-81-3 C00474 KEGG - C00474 SMP 700 rbt5p Yes D-Ribitol 5-phosphate C5H11O8P -2 C01068 KEGG - C01068 Neutral MF = C5H13O8P SMP 4267 rdmbzi No "N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole" C14H18N2O4 0 C05775 KEGG - C05775 SMP JLR Checked N-groups JLR 2726 rhcys No S-Ribosyl-L-homocysteine C9H17NO6S 0 37558-16-0 C03539 KEGG - C03539 Neutral-C9H17NO6S JLR Checked N-groups JLR 1080 rib-D No D-Ribose C5H10O5 0 50-69-1 C00121 KEGG - C00121 Neutral Compound SMP CHS 303 ribflv No Riboflavin C17H20N4O6 0 83-88-5 C00255 KEGG - C00255 Neutral Compound SMP CHS 726 rml No L-Rhamnulose C6H12O5 0 C00861 KEGG - C00861 SMP 898 rml1p No L-Rhamnulose 1-phosphate C6H11O8P -2 C01131 KEGG - C01131 Neutral MF = C6H13O8P SMP 121 rmn No L-Rhamnose C6H12O5 0 3615-41-6 C00507 KEGG - C00507 SMP 261 ru5p-D No D-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C00199 KEGG - C00199 Neutral MF = C5H11O8P Error in Chemfinder molecular formula SMP CHS 880 ru5p-L No L-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C01101 KEGG - C01101 Neutral MF = C5H11O8P SMP 140 s7p No Sedoheptulose 7-phosphate C7H13O10P -2 None C00281 KEGG - C00281 Neutral MF = C7H15O10P SMP CHS 271 sarcs Yes Sarcosine C3H7NO2 0 107-97-1 C00213 KEGG - C00213 SAB 876 sbt6p No D-Sorbitol 6-phosphate C6H13O9P -2 108392-12-7 C01096 KEGG - C01096 Neutral MF = C6H15O9P SMP CHS 645 sbt-D Yes D-Sorbitol C6H14O6 0 50-70-4 C00794 KEGG - C00794 Neutral Compound SMP CHS 2375 sbzcoa No O-Succinylbenzoyl-CoA C32H39N7O20P3S -5 C03160 KEGG - C03160 Neutral MF = C32H44N7O20P3S SMP CHS 4270 scl Yes sirohydrochlorin C42H39N4O16 -7 C05778 "KEGG - C05778 Neutral MF = C42H46N4O16 SMP Checked N-groups, JLR" 3735 scsertrna Yes L-Selenocysteinyl-tRNA(Ser) C3H6NO2R 1 16561-29-8 C05173 KEGG - C05173 1247 seln No Selenide HSe -1 531-44-2 C01528 KEGG - C01528 Neutral-H2Se JLR 3734 selnp No Selenophosphate H2O3PSe -1 16561-29-8 C05172 KEGG - C05172 Neutral H3O3PSe JLR 11861 seramp No L-seryl-AMP C13H19N6O9P 0 See EcoCyc- L-seryl-AMP JLR Checked N-groups JLR 512 ser-D No D-Serine C3H7NO3 0 312-84-5 C00740 KEGG - C00740 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR 339 ser-L No L-Serine C3H7NO3 0 56-45-1 C00065 KEGG - C00065 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR 7102 sertrna Yes L-Seryl-tRNA(Ser) C3H6NO2R 1 C02553 KEGG - C02553 SMP adjusted for Genomatica's change to aa - NCD 9015 Sfglutth Yes S-Formylglutathione C11H16N3O7S -1 C01031 "KEGG - C01031 NCD changed to protonated form, added +1 charge - NCD" 517 sheme No Siroheme C42H36FeN4O16 -8 C00748 "KEGG - C00748 Neutral MF = C42H46FeN4O16 Chemfinder formula is incorrect SMP CHS Checked N-groups, removed H from two N's in ring, JLR" 107 skm No Shikimate C7H9O5 -1 138-59-0 C00493 KEGG - C00493 Neutral MF = C7H10O5 SMP CHS 2188 skm5p No Shikimate 5-phosphate C7H8O8P -3 C03175 KEGG - C03175 Neutral MF = C7H11O8P SMP CHS 2690 sl26da No "N-Succinyl-LL-2,6-diaminoheptanedioate" C11H16N2O7 -2 C04421 KEGG - C04421 Neutral MF = C11H18N2O7 SMP CHS Changed according to Genomatica JLR 3943 sl2a6o No N-Succinyl-2-L-amino-6-oxoheptanedioate C11H12NO8 -3 C04462 KEGG - C04462 Neutral MF = C11H15NO8 SMP CHS Checked N-groups JLR 22358 so2 Yes sulfur dioxide O2S 0 C09306 AMF 1060 so3 No Sulfite O3S -2 7782-99-2 C00094 KEGG - C00094 Neutral MF = H2O3S (sulfurous acid) SMP CHS 335 so4 No Sulfate O4S -2 7664-93-9 C00059 KEGG - C00059 Neutral MF = H2O4S (sulfuric acid) SMP CHS 161 spmd No Spermidine C7H22N3 3 124-20-9 C00315 KEGG - C00315 Neutral Compound SMP CHS Changed according to Genomatica JLR 4303 ssaltpp No Succinate semialdehyde-thiamin diphosphate anion C16H21N4O10P2S -3 C05816 KEGG - C05816 Neutral MF = C16H24N4O10P2S SMP JLR Checked N-groups JLR 8781 stcoa Yes Stearoyl-CoA (n-C18:0CoA) C39H66N7O17P3S -4 362-66-3 C00412 KEGG - C00412 NCD SMP (2/7/03) C18:0 + CoA 1860 suc6p No Sucrose 6-phosphate C12H21O14P -2 C02591 KEGG - C02591 Neutral MF = C12H23O14P SMP CHS 2466 sucarg No N2-Succinyl-L-arginine C10H17N4O5 -1 1758-80-1 C03296 KEGG - C03296 Neutral:C10H18N4O5 JLR Checked N-groups JLR 2052 sucbz No o-Succinylbenzoate C11H8O5 -2 C02730 KEGG - C02730 Neutral MF = C11H10O5 SMP CHS 325 succ No Succinate C4H4O4 -2 110-15-6 C00042 KEGG - C00042 Neutral MF = C4H6O4 SMP CHS 1058 succoa No Succinyl-CoA C25H35N7O19P3S -5 604-98-8 C00091 KEGG - C00091 Neutral MF = C25H40N7O19P3S SMP CHS checked N groups - NCD 4396 sucglu No N2-Succinyl-L-glutamate C9H10NO7 -3 2009-64-5 C05931 KEGG - C05931 Neutral: C9H13NO7 JLR Checked N-groups JLR 10684 sucgsa No N2-Succinyl-L-glutamate 5-semialdehyde C9H11NO6 -2 2009-64-5 C05932 KEGG - C05932 Neutral: C9H13NO6 JLR Checked N-groups JLR 890 suchms No O-Succinyl-L-homoserine C8H12NO6 -1 1492-23-5 C01118 KEGG - C01118 Neutral MF = C8H13NO6 SMP CHS Changed according to Genomatica JLR 11414 sucorn No N2-Succinyl-L-ornithine C9H15N2O5 -1 80102-04-1 C03415 KEGG - C03415 Neutral: C9H16N2O5 JLR Checked N-groups JLR 1056 sucr Yes Sucrose C12H22O11 0 57-50-1 C00089 KEGG - C00089 284 sucsal No Succinic semialdehyde C4H5O3 -1 692-29-5 C00232 KEGG - C00232 Neutral MF = C4H6O3 SMP CHS 22150 sulfac Yes sulfoacetate C2H2O5S -2 AMF 26049 t3c11vaceACP Yes trans-3-cis-11-vacceoyl-[acyl-carrier protein] C29H51N2O8PRS -1 AMF 26047 t3c5ddeceACP Yes trans-3-cis-5-dodecenoyl-[acyl-carrier protein] C23H39N2O8PRS -1 AMF 26041 t3c7mrseACP Yes trans-3-cis-7-myristoleoyl-[acyl-carrier protein] C25H43N2O8PRS -1 AMF 26048 t3c9palmeACP Yes trans-3-cis-9-palmitoleoyl-[acyl-carrier protein] C27H47N2O8PRS -1 AMF 6458 tag6p-D No D-Tagatose 6-phosphate C6H11O9P -2 C01097 KEGG - C01097 Neutral MF=C6H13O9P JLR 11517 tagdp-D No "D-Tagatose 1,6-biphosphate" C6H10O12P2 -4 C03785 KEGG - C03785 Neutral MF = C6H14O12P2 NCD 379 tagur No D-Tagaturonate C6H9O7 -1 None C00558 KEGG - C00558 Neutral MF = C6H10O7 SMP CHS 746 tartr-L No L-tartrate C4H4O6 -2 87-69-4 C00898 KEGG - C00898 Neutral-C4H6O6 JLR 293 taur No Taurine C2H7NO3S 0 107-35-7 C00245 KEGG - C00245 Neutral MF = C2H7NO3S SMP Changed according to Genomatica JLR 1428 tcynt No Thiocyanate CNS -1 463-56-9 C01755 KEGG - C01755 Neutral-CHNS JLR Checked N-groups JLR 3802 td2coa Yes trans-Tetradec-2-enoyl-CoA C35H56N7O17P3S -4 C05273 KEGG - C05273 Neutral MF = C35H60N7O17P3S SMP 1862 tdcoa Yes Tetradecanoyl-CoA (n-C14:0CoA) C35H58N7O17P3S -4 C02593 KEGG - C02593 Neutral MF = C35H62N7O17P3S SMP changed compound class from peptides to fatty acids - NCD 4251 tddec2eACP Yes trans-Dodec-2-enoyl-[acyl-carrier protein] C23H41N2O8PRS -1 8/6/7783 C05758 KEGG - C05758 AMF 5939 tdeACP No cis-tetradec-7-enoyl-[acyl-carrier protein] (n-C14:1) C25H45N2O8PRS -1 "tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) AMF" 4248 tdec2eACP Yes trans-Dec-2-enoyl-[acyl-carrier protein] C21H37N2O8PRS -1 8/6/7783 C05754 KEGG - C05754 AMF 8779 tdecoa Yes Tetradecenoyl-CoA (n-C14:1CoA) C35H56N7O17P3S -4 NCD 3035 thdp No "2,3,4,5-Tetrahydrodipicolinate" C7H7NO4 -2 52-52-8 C03972 KEGG - C03972 Neutral MF = C7H9NO4 SMP CHS Checked N-groups JLR 4243 thex2eACP Yes trans-Hex-2-enoyl-[acyl-carrier protein] C17H29N2O8PRS -1 8/6/7783 C05748 KEGG - C05748 AMF 1065 thf No "5,6,7,8-Tetrahydrofolate" C19H21N7O6 -2 135-16-0 C00101 "KEGG - C00101 Merged with C03041 Neutral MF = C19H23N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR" 210 thm No Thiamin C12H17N4OS 1 67-03-8 C00378 KEGG - C00378 +1 Charged Compound SMP CHS neutral forumula was originally listed - NCD Changed according to Genomatica JLR 866 thmmp No Thiamin monophosphate C12H16N4O4PS -1 532-40-1 C01081 KEGG - C01081 +1 Charged MF = C12H18N4O4PS SMP CHS Checked N-groups JLR 341 thmpp No Thiamine diphosphate C12H16N4O7P2S -2 154-87-0 C00068 KEGG - C00068 Neutral MF = C12H19N4O7P2S SMP CHS Changed charged formula; had wrong number of hydrogens -NCD Checked N-groups JLR 662 thr-D Yes D-Threonine C4H9NO3 0 632-20-2 C00820 KEGG - C00820 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR 253 thr-L No L-Threonine C4H9NO3 0 72-19-5 C00188 KEGG - C00188 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR 16068 thrp Yes L-Threonine O-3-phosphate C4H8NO6P -2 C12147 AMF C12147 7108 thrtrna Yes L-Threonyl-tRNA(Thr) C4H8NO2R 1 C02992 KEGG - C02992 SMP adjusted for Genomatica's change to aa - NCD 246 thym No Thymine C5H6N2O2 0 65-71-4 C00178 KEGG - C00178 Neutral Compound SMP CHS 5269 thymd No Thymidine C10H14N2O5 0 50-89-5 C00214 KEGG - C00214 Neutral Compound SMP CHS Checked N-groups JLR 383 tma No trimethylamine C3H10N 1 75-50-3 C00565 KEGG - C00565 pKa=9.8 Checked N-groups JLR 882 tmao No Trimethylamine N-oxide C3H9NO 0 1184-78-7 C01104 "KEGG - C01104 Zwitter ion, pKa =4.65 Checked N-groups JLR" 4252 tmrs2eACP Yes trans-Tetradec-2-enoyl-[acyl-carrier protein] C25H45N2O8PRS -1 8/6/7783 C05760 KEGG - C05760 AMF 11005 toct2eACP Yes trans-Oct-2-enoyl-[acyl-carrier protein] C19H33N2O8PRS -1 8/6/7783 C05751 KEGG - C05751 AMF 26131 toctd2eACP Yes trans-octadec-2-enoyl-[acyl-carrier protein] C29H53N2O8PRS -1 AMF 4255 tpalm2eACP Yes trans-Hexadec-2-enoyl-[acyl-carrier protein] C27H49N2O8PRS -1 8/6/7783 C05763 KEGG - C05763 AMF 181 trdox No Oxidized thioredoxin X 0 C00343 KEGG - C00343 SMP 180 trdrd No Reduced thioredoxin XH2 0 C00342 KEGG - C00342 SMP 867 tre No Trehalose C12H22O11 0 99-20-7 C01083 KEGG - C01083 Neutral Compound SMP 454 tre6p No "alpha,alpha'-Trehalose 6-phosphate" C12H21O14P -2 4484-88-2 C00689 KEGG - C00689 Neutral MF = C12H23O14P SMP CHS 7097 trnaala Yes tRNA(Ala) R 0 C01635 KEGG - C01635 SMP 1333 trnaarg Yes tRNA(Arg) R 0 C01636 KEGG - C01636 SMP 11133 trnaasn Yes tRNA(Asn) R 0 C01637 KEGG - C01637 SMP 1334 trnaasp Yes tRNA(Asp) R 0 C01638 KEGG - C01638 SMP 1335 trnacys Yes tRNA(Cys) R 0 C01639 KEGG - C01639 SMP 1336 trnagln Yes tRNA(Gln) R 0 C01640 KEGG - C01640 SMP 46 trnaglu No tRNA (Glu) R 0 None C01641 "KEGG - C01641 X = (C5H8O6PR)n Represent as uncharged species SMP; MF changed on May 7, 2002 CHS" 1337 trnagly Yes tRNA(Gly) R 0 C01642 KEGG - C01642 SMP 1338 trnahis Yes tRNA(His) R 0 C01643 KEGG - C01643 SMP 1339 trnaile Yes tRNA(Ile) R 0 C01644 KEGG - C01644 SMP 1340 trnaleu Yes tRNA(Leu) R 0 C01645 KEGG - C01645 SMP 11123 trnalys Yes tRNA(Lys) R 0 C01646 KEGG - C01646 SMP 1341 trnamet Yes tRNA(Met) R 0 C01647 KEGG - C01647 SMP 1342 trnaphe Yes tRNA(Phe) R 0 C01648 KEGG - C01648 SMP 1343 trnapro Yes tRNA(Pro) R 0 C01649 KEGG - C01649 SMP 15987 trnasecys Yes tRNA(SeCys) R 0 7625-23-2 0 1344 trnaser Yes tRNA(Ser) R 0 C01650 KEGG - C01650 SMP 1345 trnathr Yes tRNA(Thr) R 0 C01651 KEGG - C01651 SMP 1346 trnatrp Yes tRNA(Trp) R 0 C01652 KEGG - C01652 SMP 7092 trnatyr Yes tRNA(Tyr) R 0 C00787 KEGG - C00787 SMP 1347 trnaval Yes tRNA(Val) R 0 C01653 KEGG - C01653 SMP 1047 trp-L No L-Tryptophan C11H12N2O2 0 73-22-3 C00078 KEGG - C00078 Neutral MF = C11H12N2O2 SMP CHS Changed according to Genomatica JLR 7113 trptrna Yes L-Tryptophanyl-tRNA(Trp) C11H11N2OR 1 C03512 KEGG - C03512 SMP adjusted for Genomatica's change to aa - NCD 164 tsul No Thiosulfate O3S2 -2 C00320 KEGG - C00320 Neutral MF = H2O3S2 SMP 6302 ttdca No tetradecanoate (n-C14:0) C14H27O2 -1 544-63-8 C06424 "KEGG C06424 Neutral MF = C14H28O2 SMP saturated fatty acid, 14 carbons changed compound class from peptides to fatty acid - NCD" 8772 ttdcea No tetradecenoate (n-C14:1) C14H25O2 -1 "monounsaturated fatty acid, 14 carbons NCD" 16112 tungs Yes tungstate O4W1 -2 AMF 100 tym Yes Tyramine C8H12NO 1 51-67-2 C00483 KEGG - C00483 AMF 1051 tyr-L No L-Tyrosine C9H11NO3 0 60-18-4 C00082 KEGG - C00082 Neutral MF = C9H11NO3 SMP CHS Changed according to Genomatica JLR 5421 tyrp Yes Phosphotyrosine C9H10NO6P -2 7625-23-2 C06501 KEGG - C06501 7105 tyrtrna Yes L-Tyrosyl-tRNA(Tyr) C9H10NO2R 1 C02839 KEGG - C02839 SMP adjusted for Genomatica's change to aa - NCD 3329 u23ga No "UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine" C43H75N3O20P2 -2 C04652 KEGG - C04652 Neutral MF = C43H77N3O20P2 SMP CHS Checked N-groups JLR 10924 u3aga No UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine C31H51N3O19P2 -2 C04738 KEGG - C04738 Neutral MF = C31H53N3O19P2 SMP CHS Checked N-groups JLR 4462 u3hga No UDP-3-O-(3-hydroxytetradecanoyl)-D-glucosamine C29H50N3O18P2 -1 C06022 KEGG - C06022 Neutral MF = C29H51N3O18P2 SMP CHS Checked N-groups JLR 4370 uaagmda No "Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala" C95H152N8O28P2 -4 C05898 KEGG - C05898 Neutral MF = C95H156N8O28P2 SMP Changed according to Genomatica JLR 3312 uaccg No UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine C20H26N3O19P2 -3 C04631 KEGG - C04631 Neutral MF = C20H29N3O19P2 SMP CHS Checked N-groups JLR 326 uacgam No UDP-N-acetyl-D-glucosamine C17H25N3O17P2 -2 C00043 KEGG - C00043 KEGG glycan: G10610 Neutral MF = C17H27N3O17P2 SMP CHS Checked N-groups JLR 764 uacmam No UDP-N-acetyl-D-mannosamine C17H25N3O17P2 -2 C01170 KEGG - C01170 Neutral MF = C17H27N3O17P2 SMP CHS Kegg Picture is missing the N on the 2-C of the sugar Checked N-groups JLR 4636 uacmamu No UDP-N-acetyl-D-mannosaminouronate C17H22N3O18P2 -3 90-02-8 C06240 KEGG - C06240 Neutral-C17H25N3O18P2 JLR Checked N-groups JLR 4369 uagmda No "Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine" C87H139N7O23P2 -4 C05897 KEGG - C05897 Neutral MF = C87H143N7O23P2 SMP Changed according to Genomatica JLR 942 uama No UDP-N-acetylmuramoyl-L-alanine C23H33N4O20P2 -3 C01212 KEGG - C01212 Neutral MF = C23H36N4O20P2 SMP CHS Checked N-groups JLR 456 uamag No UDP-N-acetylmuramoyl-L-alanyl-D-glutamate C28H39N5O23P2 -4 C00692 KEGG - C00692 Neutral MF = C28H43N5O23P2 SMP CHS Checked N-groups JLR 686 uamr No UDP-N-acetylmuramate C20H28N3O19P2 -3 C01050 KEGG - C01050 Neutral MF = C20H31N3O19P2 SMP CHS Checked N-groups JLR 2729 udcpdp No Undecaprenyl diphosphate C55H89O7P2 -3 C03543 KEGG - C03543 Neutral MF = C55H92O7P2 SMP CHS 185 udcpp No Undecaprenyl phosphate C55H89O4P -2 C00348 KEGG - C00348 Neutral MF = C55H91O4P SMP CHS 477 udp No UDP C9H11N2O12P2 -3 58-98-0 C00015 KEGG - C00015 Neutral MF = C9H14N2O12P2 SMP CHS 10912 udpacgal Yes UDP-N-acetyl-D-galactosamine C17H25N3O17P2 -2 None C00203 KEGG - C00203 changed to proper charge - NCD 316 udpg No UDPglucose C15H22N2O17P2 -2 C00029 KEGG - C00029 Neutral MF = C15H24N2O17P2 SMP CHS 331 udpgal No UDPgalactose C15H22N2O17P2 -2 C00052 KEGG - C00052 Neutral MF = C15H24N2O17P2 SMP CHS 1996 udpgalfur No "UDP-D-galacto-1,4-furanose" C15H22N2O17P2 -2 638-23-3 C03733 KEGG - C03733 Neutral-C15H24N2O17P2 JLR Checked N-groups JLR 241 udpglcur No UDP-D-glucuronate C15H19N2O18P2 -3 C00167 KEGG - C00167 Neutral-C15H22N2O18P2 JLR Checked N-groups JLR 22054 udpLa4fn Yes uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose C15H21N3O16P2 -2 AMF 22046 udpLa4n Yes uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose C14H22N3O15P2 -1 AMF 22045 udpLa4o Yes UDP-4-keto-pyranose C14H18N2O16P2 -2 AMF 10726 ugmd No "UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate" C35H51N7O26P2 -4 C04877 KEGG - C04877 Neutral MF = C35H55N7O26P2 SMP Changed according to Genomatica JLR 3599 ugmda No "UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine" C41H61N9O28P2 -4 C04882 KEGG - C04882 Neutral MF = C41H65N9O28P2 SMP Changed according to Genomatica JLR 22056 uLa4fn Yes undecaprenyl phosphate-4-amino-4-formyl-L-arabinose C61H99N1O8P1 -1 AMF 22047 uLa4n Yes undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose C60H100N1O7P1 0 AMF 21516 um4p Yes "UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine" C38H56N8O27P2 -4 AMF 1068 ump No UMP C9H11N2O9P -2 58-97-9 C00105 KEGG - C00105 Neutral MF = C9H13N2O9P SMP CHS 9105 unaga No Undecaprenyl diphospho N-acetyl-glucosamine C63H103NO12P2 -2 Not in Kegg Neutral-C63H105NO12P2 JLR Checked N-groups 9106 unagamu No Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate C71H113N2O18P2 -3 No Kegg entry Neutral-C71H116N2O18P2 JLR Checked N-groups JLR 9111 unagamuf No "Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose" C79H126N3O22P2 -3 No Kegg entry Neutral-C79H129N3O22P2 JLR Checked N-groups JLR 687 uppg3 No Uroporphyrinogen III C40H36N4O16 -8 1976-85-8 C01051 KEGG - C01051 Neutral MF = C40H44N4O16 SMP CHS Checked N-groups JLR 1069 ura No Uracil C4H4N2O2 0 66-22-8 C00106 KEGG - C00106 Neutral Compound SMP CHS 199 urate Yes Urate C5H4N4O3 0 69-93-2 C00366 KEGG - C00366 Neutral Compound SMP CHS 9076 urdglyc No (-)-Ureidoglycolate C3H5N2O4 -1 C00603 KEGG - C00603 Neutral- C4H6N2O4 JLR Checked N-groups JLR 1054 urea No Urea CH4N2O 0 57-13-6 C00086 KEGG - C00086 Neutral Compound SMP CHS Checked N-groups JLR 10727 uri No Uridine C9H12N2O6 0 58-96-8 C00299 KEGG - C00299 Neutral Compound SMP CHS Checked N-groups JLR 345 utp No UTP C9H11N2O15P3 -4 63-39-8 C00075 KEGG - C00075 Neutral MF = C9H15N2O15P3 SMP CHS 250 val-L No L-Valine C5H11NO2 0 72-18-4 C00183 KEGG - C00183 Neutral MF = C5H11NO2 SMP CHS Changed according to Genomatica JLR 7103 valtrna Yes L-Valyl-tRNA(Val) C5H10NOR 1 C02554 KEGG - C02554 SMP adjusted for Genomatica's change to aa - NCD 216 xan No Xanthine C5H4N4O2 0 69-89-6 C00385 KEGG - C00385 Neutral Compound SMP CHS Checked N-groups JLR 1028 xdp Yes XDP C10H11N4O12P2 -3 7440-23-5 C01337 KEGG - C01337 AMF 436 xmp No Xanthosine 5'-phosphate C10H11N4O9P -2 523-98-8 C00655 KEGG - C00655 Neutral MF = C10H13N4O9P SMP CHS Checked N-groups JLR 459 xtp Yes XTP C10H11N4O15P3 -4 C00700 KEGG - C00700 IT 10906 xtsn No Xanthosine C10H12N4O6 0 146-80-5 C01762 KEGG - C01762 Neutral Compound SMP CHS Checked N-groups JLR 283 xu5p-D No D-Xylulose 5-phosphate C5H9O8P -2 None C00231 KEGG - C00231 Neutral MF = C5H11O8P SMP CHS 2462 xu5p-L No L-Xylulose 5-phosphate C5H9O8P -2 None C03291 KEGG - C03291 Neutral MF = C5H11O8P Different from xu5p-D (C00231): Change abbv from xu5p to x5p-L SMP CHS 248 xyl-D No D-Xylose C5H10O5 0 58-86-6 C00181 KEGG - C00181 Neutral Compound SMP CHS 157 xylu-D No D-Xylulose C5H10O5 0 551-84-8 C00310 KEGG - C00310 Neutral Compound SMP CHS 159 xylu-L Yes L-Xylulose C5H10O5 0 527-50-4 C00312 KEGG - C00312 Neutral Compound SMP CHS 324 zn2 Yes Zinc Zn 2 7440-66-6 C00038 KEGG - C00038