abbreviation officialName formula charge casNumber KEGG cmpd ID notes 10fthf 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 12dgr_EC 1,2-Diacylglycerol (E.coli) C1836H3448O250 0 tv org: Hpylori, Ecoli 12dgr scaled up (50x) with 2 ave fatty acids. 12ppd-S (S)-Propane-1,2-diol C3H8O2 0 4254-14-2 C02917 KEGG - C02917 SMP CHS 13dpg 3-Phospho-D-glyceroyl phosphate C3H4O10P2 -4 None C00236 KEGG - C00236 Neutral MF = C3H8O10P2 SMP CHS 14glucan 1,4-alpha-D-glucan C36H62O31 0 AMF made up formula to match malthx, the highest carbon maltodextrin that is transported in the model 15dap 1,5-Diaminopentane C5H16N2 2 462-94-2 C01672 KEGG - C01672 Neutral Compound SMP CHS Changed according to Genomatica JLR 1pyr5c 1-Pyrroline-5-carboxylate C5H6NO2 -1 C03912 KEGG - C03912 Neutral MF = C5H7NO2 SMP CHS Checked N-groups JLR,NCD 23camp 2',3'-Cyclic AMP C10H11N5O6P -1 9014-63-5 C02353 KEGG - C02353 AMF 23ccmp 2',3'-Cyclic CMP C9H11N3O7P -1 C02354 KEGG - C02354 AMF 23cgmp 2',3'-Cyclic GMP C10H11N5O7P -1 C06194 KEGG - C06194 AMF 23cump 2',3'-Cyclic UMP C9H10N2O8P -1 9014-63-5 C02355 KEGG - C02355 AMF 23dappa 2,3-diaminopropionate C3H9N2O2 1 C06393 MKA L- and D- forms not distinguished here 23ddhb 2,3-Dihydro-2,3-dihydroxybenzoate C7H7O4 -1 C04171 KEGG - C04171 Neutral MF = C7H8O4 SMP CHS 23dhb 2,3-Dihydroxybenzoate C7H5O4 -1 303-38-8 C00196 KEGG - C00196 Neutral MF = C7H6O4 SMP CHS 23dhba (2,3-Dihydroxybenzoyl)adenylate C17H17N5O10P -1 C04030 KEGG - C04030 Neutral MF = C17H18N5O10P SMP CHS Check groups AMF, JLR, SAB 23dhbzs 2,3-dihydroxybenzoylserine C10H10NO6 -1 AMF 23dhdp 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 23dhmb (R)-2,3-Dihydroxy-3-methylbutanoate C5H9O4 -1 C04272 KEGG - C04272 (C04039 Deleted) Neutral MF = C5H10O4 SMP CHS 23dhmp (R)-2,3-Dihydroxy-3-methylpentanoate C6H11O4 -1 C06007 KEGG - C06007 (C04104 Deleted) Neutral MF = C6H12O4 SMP CHS 23doguln 2,3-Dioxo-L-gulonate C6H7O7 -1 583-08-4 C05409 KEGG - C05409 Neutral-C6H8O7 JLR 25aics (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 25dkglcn 2,5-diketo-D-gluconate C6H7O7 -1 C02780 KEGG C02780 Neutal - C6H8O7 JLR 25drapp 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 26dap-LL LL-2,6-Diaminoheptanedioate C7H14N2O4 0 583-93-7 C00666 KEGG - C00666 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR 26dap-M meso-2,6-Diaminoheptanedioate C7H14N2O4 0 None C00680 KEGG - C00680 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR 2ahbut (S)-2-Aceto-2-hydroxybutanoate C6H9O4 -1 C06006 KEGG - C06006 (C00659 Deleted) Neutral MF = C6H10O4 SMP CHS 2amsa 2-Aminomalonate semialdehyde C3H5NO3 0 C11822 0 2aobut L-2-Amino-3-oxobutanoate C4H7NO3 0 C03508 KEGG - C03508 (C03214 Deleted) Neutral MF = C4H7NO3 SMP CHS Checked N-groups JLR 2cpr5p 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate C12H13NO9P -3 C01302 KEGG - C01302 Neutral MF = C12H16NO9P SMP Checked N-groups JLR 2dda7p 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate C7H10O10P -3 C04691 KEGG - C04691 Neutral MF = C7H13O10P SMP CHS 2ddg6p 2-Dehydro-3-deoxy-D-gluconate 6-phosphate C6H8O9P -3 C04442 KEGG - C04442 Neutral MF = C6H11O9P SMP CHS 2ddglcn 2-Dehydro-3-deoxy-D-gluconate C6H9O6 -1 None C00204 KEGG - C00204 Neutral MF = C6H10O6 SMP CHS 2dh3dgal 2-Dehydro-3-deoxy-D-galactonate C6H9O6 -1 C01216 KEGG - C01216 Neutral-C6H10O6 JLR 2dh3dgal6p 2-Dehydro-3-deoxy-D-galactonate 6-phosphate C6H8O9P -3 C01286 KEGG - C01286 Neutral-C6H11O9P JLR 2dhglcn 2-Dehydro-D-gluconate C6H9O7 -1 C00629 KEGG - C00629 Neutral-C6H10O7 JLR 2dhguln 2-Dehydro-L-gulonate C6H9O7 -1 No Kegg entry Neutral- C6H10O7 JLR 2dhp 2-Dehydropantoate C6H9O4 -1 C00966 KEGG - C00966 Neutral MF = C6H10O4 SMP CHS 2dmmq8 2-Demethylmenaquinone 8 C50H70O2 0 C05818 KEGG - C05818 General Formula = C15H14O2(C5H8)n; n = 7 for 2dmmq8 SMP 2dmmql8 2-Demethylmenaquinol 8 C50H72O2 0 JLR 2dr1p 2-Deoxy-D-ribose 1-phosphate C5H9O7P -2 C00672 KEGG - C00672 Neutral MF = C5H11O7P SMP CHS 2dr5p 2-Deoxy-D-ribose 5-phosphate C5H9O7P -2 102916-66-5 C00673 KEGG - C00673 Neutral MF = C5H11O7P SMP CHS 2h3oppan 2-Hydroxy-3-oxopropanoate C3H3O4 -1 C01146 KEGG - C01146 Neutral-C3H4O4 JLR 2ippm 2-Isopropylmaleate C7H8O4 -2 C02631 KEGG - C02631 Neutral MF = C7H10O4 SMP 2kmb 2-keto-4-methylthiobutyrate C5H7O3S -1 No KEGG Entry JEM has it as KMB Neutral MF = C5H8O3S SMP 2mahmp 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate C6H8N3O7P2 -3 745-65-3 C04752 KEGG - C04752 Neutral MF = C6H11N3O7P2 SMP Checked N-groups JLR 2mcacn cis-2-Methylaconitate C7H5O6 -3 99-98-9 C04225 KEGG - C04225 Neutral-C7H8O6 JLR 2mcit 2-Methylcitrate C7H7O7 -3 96-17-3 C02225 KEGG - C02225 NCD JLR 2me4p 2-C-methyl-D-erythritol 4-phosphate C5H11O7P -2 C11434 KEGG C11434 Neutral MF = C5H13O7P SMP 2mecdp 2-C-methyl-D-erythritol 2,4-cyclodiphosphate C5H10O9P2 -2 C11453 KEGG ID- C11453 Neutral MF = C5H12O9P2 SMP 2obut 2-Oxobutanoate C4H5O3 -1 600-18-0 C00109 KEGG - C00109 Neutral MF = C4H6O3 SMP CHS NCD 2ohph 2-Octaprenyl-6-hydroxyphenol C46H70O2 0 C05811 KEGG - C05811 SMP CHS 2ombzl 2-Octaprenyl-6-methoxy-1,4-benzoquinol C47H72O3 0 Neidhardt page 651 JLR 2omhmbl 2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol C48H74O4 0 Neidhardt page 651 JLR 2ommbl 2-Octaprenyl-3-methyl-6-methoxy- 1,4-benzoquinol C48H74O3 0 Neidhardt page 651 JLR 2omph 2-Octaprenyl-6-methoxyphenol C47H72O2 0 C05812 KEGG - C05812 SMP CHS 2oph 2-Octaprenylphenol C46H70O 0 C05810 KEGG - C05810 SMP CHS 2p4c2me 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H22N3O17P3 -4 No KEGG Entry Neutral MF = C14H26N3O17P3 SMP Checked N-groups JLR 2pg D-Glycerate 2-phosphate C3H4O7P -3 C00631 KEGG - C00631 Neutral MF = C3H7O7P SMP CHS 2pglyc 2-Phosphoglycolate C2H2O6P -3 C00988 KEGG - C00988 Neutral MF = C2H5O6P SMP CHS 2shchc 2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate C11H10O6 -2 C05817 KEGG - C05817 Neutral MF = C11H12O6 SMP CHS 2tpr3dpcoa 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA C26H40N7O26P5S -6 AMF 34dhpac 3,4-Dihydroxyphenylacetaldehyde C8H8O3 0 145-14-2 C04043 KEGG - C04043 SAB 34hpp 3-(4-Hydroxyphenyl)pyruvate C9H7O4 -1 C01179 KEGG - C01179 Neutral MF = C9H8O4 SMP CHS 3amp 3'-AMP C10H12N5O7P -2 84-21-9 C01367 MKA AMF 3c2hmp 3-Carboxy-2-hydroxy-4-methylpentanoate C7H10O5 -2 C04411 KEGG - C04411 Neutral MF = C7H12O5 SMP CHS 3c3hmp 3-Carboxy-3-hydroxy-4-methylpentanoate C7H10O5 -2 C02504 KEGG - C02504 Neutral MF = C7H12O5 SMP CHS 3c4mop 3-Carboxy-4-methyl-2-oxopentanoate C7H8O5 -2 C04236 KEGG - C04236 Neutral MF = C7H10O5 SMP 3cmp 3'-cmp C9H12N3O8P -2 C05822 MKA AMF 3dhguln 3-Dehydro-L-gulonate C6H9O7 -1 C00618 KEGG - C00618 Neutral-C6H10O7 JLR NCD MKA 3dhgulnp 3-keto-L-gulonate-6-phosphate C6H8O10P -3 No Kegg entry Neutral-C6H11O10P JLR 3dhq 3-Dehydroquinate C7H9O6 -1 C00944 KEGG - C00944 Neutral MF = C7H10O6 SMP CHS 3dhsk 3-Dehydroshikimate C7H7O5 -1 10457-99-5 C02637 KEGG - C02637 Neutral MF = C7H8O5 SMP CHS 3gmp 3'-GMP C10H12N5O8P -2 497-76-7 C06193 KEGG - C06193 AMF 3hbcoa (S)-3-Hydroxybutanoyl-CoA C25H38N7O18P3S -4 C01144 KEGG - C01144 Neutral MF = C25H42N7O18P3S SMP 3hcinnm 3-hydroxycinnamic acid C9H7O3 -1 No Kegg entry see PMID: 9603882 Neutral-C9H8O3 JLR 3hdcoa (S)-3-Hydroxydecanoyl-CoA C31H50N7O18P3S -4 C05264 KEGG - C05264 Neutral MF = C31H54N7O18P3S SMP 3hddcoa (S)-3-Hydroxydodecanoyl-CoA C33H54N7O18P3S -4 C05262 KEGG - C05262 Neutral MF = C33H58N7O18P3S SMP 3hhcoa (S)-3-Hydroxyhexanoyl-CoA C27H42N7O18P3S -4 C05268 KEGG - C05268 Neutral MF = C27H46N7O18P3S SMP 3hhdcoa (S)-3-Hydroxyhexadecanoyl-CoA C37H62N7O18P3S -4 C05258 KEGG - C05258 Neutral MF = C37H66N7O18P3S SMP 3hmrsACP R-3-hydroxy-myristoyl-ACP C25H47N2O9PRS -1 Based on NH page 1040 and 615 JLR JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) 3hocoa (S)-3-Hydroxyoctanoyl-CoA C29H46N7O18P3S -4 C05266 KEGG - C05266 Neutral MF = C29H50N7O18P3S SMP 3hodcoa (S)-3-Hydroxyoctadecanoyl-CoA C39H66N7O18P3S -4 NCD 3hpppn 3-(3-hydroxy-phenyl)propionate C9H9O3 -1 No Kegg entry see PMID: 9603882 Neutral JLR 3htdcoa (S)-3-Hydroxytetradecanoyl-CoA C35H58N7O18P3S -4 C05260 KEGG - C05260 Neutral MF = C35H62N7O18P3S SMP 3ig3p C'-(3-Indolyl)-glycerol 3-phosphate C11H12NO6P -2 C03506 KEGG - C03506 Neutral MF = C11H14NO6P SMP Checked N-groups JLR 3mob 3-Methyl-2-oxobutanoate C5H7O3 -1 C00141 KEGG - C00141 Neutral MF = C5H8O3 SMP CHS 3mop (S)-3-Methyl-2-oxopentanoate C6H9O3 -1 C00671 KEGG - C00671 Neutral MF = C6H10O3 C003465 and C03911 are deleted SMP CHS 3odcoa 3-Oxodecanoyl-CoA C31H48N7O18P3S -4 C05265 KEGG - C05265 Neutral MF = C31H52N7O18P3S SMP 3oddcoa 3-Oxododecanoyl-CoA C33H52N7O18P3S -4 C05263 KEGG - C05263 Neutral MF = C33H56N7O18P3S SMP 3ohcoa 3-Oxohexanoyl-CoA C27H40N7O18P3S -4 5096-70-8 C05269 KEGG - C05269 Neutral MF = C27H44N7O18P3S SMP 3ohdcoa 3-Oxohexadecanoyl-CoA C37H60N7O18P3S -4 C05259 KEGG - C05259 Neutral MF = C37H64N7O18P3S SMP 3oocoa 3-Oxooctanoyl-CoA C29H44N7O18P3S -4 C05267 KEGG - C05267 Neutral MF = C29H48N7O18P3S SMP 3oodcoa 3-Oxooctadecanoyl-CoA C39H64N7O18P3S -4 SMP (2/7/03) 3ophb 3-Octaprenyl-4-hydroxybenzoate C47H69O3 -1 C05809 KEGG - C05809 Neutral MF = C47H70O3 SMP CHS 3otdcoa 3-Oxotetradecanoyl-CoA C35H56N7O18P3S -4 C05261 KEGG - C05261 Neutral MF = C35H60N7O18P3S SMP 3pg 3-Phospho-D-glycerate C3H4O7P -3 C00197 KEGG - C00197 Neutral MF = C3H7O7P Deleted C00597 SMP CHS 3php 3-Phosphohydroxypyruvate C3H2O7P -3 C03232 KEGG - C03232 Neutral MF = C3H5O7P SMP CHS 3psme 5-O-(1-Carboxyvinyl)-3-phosphoshikimate C10H9O10P -4 C01269 KEGG - C01269 Neutral MF = C10H13O10P SMP 3sala 3-Sulfino-L-alanine C3H5NO4S -2 1115-65-7 C00606 KEGG - C00606 Neutral MF = C3H7NO4S SMP CHS 3ump 3'-UMP C9H11N2O9P -2 35170-03-7 C01368 KEGG - C01368 AMF 4abut 4-Aminobutanoate C4H9NO2 0 56-12-2 C00334 KEGG - C00334 Neutral MF = C4H9NO2 SMP CHS Changed according to Genomatica JLR 4abutn 4-Aminobutanal C4H10NO 1 C00555 KEGG - C00555 Neutral Compound SMP CHS Changed according to Genomatica JLR 4abz 4-Aminobenzoate C7H6NO2 -1 150-13-0 C00568 KEGG - C00568 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR 4adcho 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 4ahmmp 4-Amino-5-hydroxymethyl-2-methylpyrimidine C6H9N3O 0 73-67-6 C01279 KEGG - C01279 Neutral SMP CHS Checked N-groups JLR 4ampm 4-Amino-2-methyl-5-phosphomethylpyrimidine C6H8N3O4P -2 C04556 KEGG - C04556 Neutral MF = C6H10N3O4P SMP CHS Checked N-groups JLR 4c2me 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H23N3O14P2 -2 C11435 KEGG C11435 Neutral MF = C14H25N3O14P2 SMP Checked N-groups JLR 4h2opntn 4-Hydroxy-2-oxopentanoate C5H7O4 -1 111844-33-8 C03589 KEGG - C03589 Neutral-C5H8O4 JLR 4hba 4-Hydroxy-benzyl alcohol C7H8O2 0 tv 4hbz 4-Hydroxybenzoate C7H5O3 -1 99-96-7 C00156 KEGG - C00156 Neutral MF = C7H6O3 SMP CHS 4hoxpacd 4-Hydroxyphenylacetaldehyde C8H8O2 0 60-11-7 C03765 KEGG - C03765 SAB 4hthr 4-Hydroxy-L-threonine C4H9NO4 0 C06056 KEGG C06056 JLR Checked N JLR 4mhetz 4-Methyl-5-(2-hydroxyethyl)-thiazole C6H9NOS 0 137-00-8 C04294 KEGG - C04294 Neutral SMP CHS Checked N-groups JLR 4mop 4-Methyl-2-oxopentanoate C6H9O3 -1 C00233 KEGG - C00233 Neutral MF = C6H10O3 SMP CHS 4mpetz 4-Methyl-5-(2-phosphoethyl)-thiazole C6H8NO4PS -2 C04327 KEGG - C04327 Neutral MF = C6H10NO4PS SMP CHS Checked N-groups JLR 4pasp 4-Phospho-L-aspartate C4H6NO7P -2 C03082 KEGG - C03082 Neutral MF = C4H8NO7P SMP CHS Changed according to Genomatica JLR 4per 4-Phospho-D-erythronate C4H6O8P -3 C03393 KEGG - C03393 Neutral MF = C4H9O8P SMP CHS 4ppan D-4'-Phosphopantothenate C9H15NO8P -3 C03492 KEGG - C03492 Neutral MF = C9H18NO8P SMP CHS Checked N-groups JLR 4ppcys N-((R)-4-Phosphopantothenoyl)-L-cysteine C12H20N2O9PS -3 C04352 KEGG - C04352 Neutral MF = C12H23N2O9PS SMP CHS Checked N-groups JLR 4r5au 4-(1-D-Ribitylamino)-5-aminouracil C9H16N4O6 0 C04732 KEGG - C04732 SMP Checked N-groups, agrees with ACD software, JLR 5aizc 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate C9H11N3O9P -3 C04751 KEGG - C04751 Neutral MF = C9H14N3O9P SMP CHS Checked N-groups JLR 5aop 5-Amino-4-oxopentanoate C5H9NO3 0 106-60-5 C00430 KEGG - C00430 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR 5aprbu 5-Amino-6-(5'-phosphoribitylamino)uracil C9H15N4O9P -2 C04454 KEGG - C04454 Neutral MF = C9H17N4O9P SMP Checked N-groups NCD, JLR 5apru 5-Amino-6-(5'-phosphoribosylamino)uracil C9H13N4O9P -2 C01268 KEGG - C01268 Neutral MF = C9H15N4O9P SMP Checked N-groups JLR, NCD 5caiz 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 5dglcn 5-Dehydro-D-gluconate C6H9O7 -1 C01062 KEGG - C01062 Neutral-C6H10O7 JLR 5dh4dglc 5-Dehydro-4-deoxy-D-glucarate C6H6O7 -2 C00679 KEGG - C00679 Neutral-C6H8O7 JLR 5mdr1p 5-Methylthio-5-deoxy-D-ribose 1-phosphate C6H11O7PS -2 C04188 KEGG - C04188 Neutral MF = C6H13O7PS SMP CHS 5mdru1p 5-Methylthio-5-deoxy-D-ribulose 1-phosphate C6H11O7PS -2 C04582 KEGG - C04582 Neutral MF = C6H13O7PS SMP CHS 5mta 5-Methylthioadenosine C11H15N5O3S 0 2457-80-9 C00170 KEGG - C00170 Neutral MF = C11H15N5O3S SMP CHS Checked N-groups JLR 5mthf 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 5mtr 5-Methylthio-D-ribose C6H12O4S 0 C03089 KEGG - C03089 Neutral Compound SMP CHS 5prdmbz N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole C14H17N2O7P -2 C04778 KEGG - C04778 Neutral MF = C14H19N2O7P SMP JLR Checked N-groups JLR 6hmhpt 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 6hmhptpp 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 6pgc 6-Phospho-D-gluconate C6H10O10P -3 C00345 KEGG - C00345 Neutral MF = C6H13O10P SMP CHS 6pgl 6-phospho-D-glucono-1,5-lactone C6H9O9P -2 None C01236 KEGG - C01236 Neutral MF = C6H11O9P SMP CHS 8aonn 8-Amino-7-oxononanoate C9H17NO3 0 C01092 KEGG - C01092 Neutral MF = C9H17NO3 SMP CHS Changed according to Genomatica JLR aacald Aminoacetaldehyde C2H6NO 1 452-86-8 C06735 KEGG - C06735 Checked N JLR aacoa Acetoacetyl-CoA C25H36N7O18P3S -4 1420-36-6 C00332 KEGG - C00332 Neutral MF = C25H40N7O18P3S SMP CHS aact Aminoacetone C3H8NO 1 298-08-8 C01888 KEGG - C01888 Neutral Compound SMP Checked N-groups JLR ac Acetate C2H3O2 -1 64-19-7 C00033 KEGG - C00033 Neutral MF = C2H4O2 SMP CHS acac Acetoacetate C4H5O3 -1 541-50-4 C00164 KEGG - C00164 NCD acACP Acetyl-ACP C13H23N2O8PRS -1 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) acald Acetaldehyde C2H4O 0 75-07-0 C00084 KEGG - C00084 Neutral Compound SMP CHS acanth N-Acetylanthranilate C9H8NO3 -1 89-52-1 C06332 KEGG - C06332 AMF accoa Acetyl-CoA C23H34N7O17P3S -4 72-89-9 C00024 KEGG - C00024 Neutral MF = C23H38N7O17P3S SMP CHS acg5p N-Acetyl-L-glutamyl 5-phosphate C7H9NO8P -3 C04133 KEGG - C04133 Neutral MF = C7H12NO8P SMP CHS Checked N-groups JLR acg5sa N-Acetyl-L-glutamate 5-semialdehyde C7H10NO4 -1 None C01250 KEGG - C01250 Neutral MF = C7H11NO4 SMP CHS Checked N-groups JLR acgal N-Acetyl-D-galactosamine C8H15NO6 0 14215-68-0; 1811-31-0 C01132 KEGG - C01132 Neutral Compound SMP NCD acgal1p N-Acetyl-D-galactosamine 1-phosphate C8H14NO9P -2 not in KEGG NCD acgam N-Acetyl-D-glucosamine C8H15NO6 0 7512-17-6 C00140 KEGG - C00140 Neutral Compound SMP Checked N-groups JLR acgam1p N-Acetyl-D-glucosamine 1-phosphate C8H14NO9P -2 None C04256 KEGG - C04256 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR acgam6p N-Acetyl-D-glucosamine 6-phosphate C8H14NO9P -2 102029-88-9 C00357 KEGG - C00357 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR acglc-D 6-Acetyl-D-glucose C8H14O7 0 107-85-7 C02655 KEGG - C02655 AMF acglu N-Acetyl-L-glutamate C7H9NO5 -2 1188-37-0 C00624 KEGG - C00624 Neutral MF = C7H11NO5 SMP CHS Checked N-groups JLR acmalt Acetyl-maltose C14H24O12 0 C02130 KEGG - C02130 Neutral Compound SMP acmana N-Acetyl-D-mannosamine C8H15NO6 0 3615-17-6 C00645 KEGG - C00645 Neutral Compound SMP Checked N-groups JLR acmanap N-Acetyl-D-mannosamine 6-phosphate C8H14NO9P -2 157296-99-6 C04257 KEGG - C04257 Neutral-C8H16NO9P JLR Checked N JLR acmum N-Acetylmuramate C11H18NO8 -1 61633-75-8 C02713 KEGG - C02713 JLR Checked N-Groups acmum6p N-acetylmuramate 6-phosphate C11H17NO11P -3 Not in KEGG see PMID 15060041 JLR AMF acnam N-Acetylneuraminate C11H18NO9 -1 131-48-6 C00270 KEGG - C00270 Neutral MF = C11H19NO9 SMP CHS Checked N-groups JLR acolipa 4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A C181H314N3O103P4 -9 AMF aconm E-3-carboxy-2-pentenedioate 6-methyl ester C7H6O6 -2 Not in Kegg (see PMID 11329290, figure 1) Neutral-C7H8O6 JLR acon-T trans-Aconitate C6H3O6 -3 4023-65-8 C02341 KEGG - C02341 Neutral MF = C6H6O6 SMP CHS acorn N2-Acetyl-L-ornithine C7H14N2O3 0 None C00437 KEGG - C00437 Neutral MF = C7H14N2O3 SMP CHS Changed according to Genomatica JLR ACP 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) acser O-Acetyl-L-serine C5H9NO4 0 66638-22-0 C00979 KEGG - C00979 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR actACP Acetoacetyl-ACP C15H25N2O9PRS -1 C05744 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) actp Acetyl phosphate C2H3O5P -2 19926-71-7 C00227 KEGG - C00227 Neutral MF = C2H5O5P SMP CHS acyllpp_EC acyl-lipoprotein (E. coli) XC843H1524O50 0 AMF generic acyllipoprotein ade Adenine C5H5N5 0 73-24-5 C00147 KEGG - C00147 Neutral Compound SMP CHS adn Adenosine C10H13N5O4 0 58-61-7 C00212 KEGG - C00212 Neutral Compound SMP CHS Checked N-groups JLR adocbi 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) adocbip 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) adocbl 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) adp ADP C10H12N5O10P2 -3 20398-34-9 C00008 KEGG - C00008 Neutral MF = C10H15N5O10P2 SMP CHS adpglc ADPglucose C16H23N5O15P2 -2 C00498 KEGG - C00498 Neutral MF = C16H25N5O15P2 SMP CHS adphep-D,D ADP-D-glycero-D-manno-heptose C17H25N5O16P2 -2 119-61-9 C06397 KEGG - C06397 Neutral-C17H27N5016P2 JLR Checked N JLR adphep-L,D ADP-L-glycero-D-manno-heptose C17H25N5O16P2 -2 C06398 Kegg- C06398 Neutral-C17H27N5O16P2 JLR Checked N JLR adprib ADPribose C15H21N5O14P2 -2 C00301 KEGG - C00301 Neutral MF = C15H23N5O14P2 SMP CHS checked N groups - NCD ag silver Ag 1 7440-22-4 C06710 KEGG - C06710 agdpcbi 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) agm Agmatine C5H16N4 2 306-60-5 C00179 KEGG - C00179 Neutral Compound SMP CHS Changed according to Genomatica JLR agpc_EC acyl-glycerophosphocholine C1243H2524N50O350P50 0 Scaled up by 50, really is 50 molecules or phosphatidylcholine. Scale was used so that the elements were whole numbers. JLR agpe_EC acyl-glycerophosphoethanolamine (E.coli) C1093H2224O350N50P50 0 1-acyl and 2-acyl are treated the same for simplicity Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 agpe_EC is really one molecule of agpe. JLR Checked N JLR agpg_EC acyl-glycerophosphoglycerol (E.coli) C1143H2224O450P50 -50 1-acyl and 2-acyl are treated the same for simplicity Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 agpg_EC is really one molecule of agpg. JLR ahcys S-Adenosyl-L-homocysteine C14H20N6O5S 0 979-92-0 C00021 KEGG - C00021 Neutral MF = C14H20N6O5S SMP CHS Changed according to Genomatica JLR ahdt 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 aicar 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 air 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 akg 2-Oxoglutarate C5H4O5 -2 328-50-7 C00026 KEGG - C00026 Neutral MF = C5H6O5 SMP CHS alaala D-Alanyl-D-alanine C6H12N2O3 0 923-16-0 C00993 KEGG - C00993 Neutral MF = C6H12N2O3 SMP CHS Changed according to Genomatica JLR ala-B beta-Alanine C3H7NO2 0 107-95-9 C00099 KEGG - C00099 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR alac-S (S)-2-Acetolactate C5H7O4 -1 C06010 KEGG - C06010 (C00900 Deleted) Neutral MF = C5H8O4 SMP CHS ala-D D-Alanine C3H7NO2 0 338-69-2 C00133 KEGG - C00133 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR ala-L L-Alanine C3H7NO2 0 56-41-7 C00041 KEGG - C00041 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR alatrna L-Alanyl-tRNA(Ala) C3H6NOR 1 C00886 KEGG - C00886 SMP adjusted for Genomatica's change to aa - NCD all6p D-Allose 6-phosphate C6H11O9P -2 147-94-4 C02962 KEGG - C02962 all-D D-Allose C6H12O6 0 2595-97-3 C01487 KEGG - C01487 JLR alltn Allantoin C4H6N4O3 0 97-59-6 C01551 KEGG - C01551 Neutral Compound SMP CHS Checked N-groups JLR alltt Allantoate C4H7N4O4 -1 99-16-1 C00499 KEGG - C00499 Neutral MF = C4H8N4O4 SMP CHS Checked N-groups JLR allul6p Allulose 6-phosphate C6H11O9P -2 No KEGG entry see allulose and PMID 9401019 JLR altrn D-Altronate C6H11O7 -1 C00817 KEGG - C00817 Neutral MF = C6H12O7 No L-altronate found in Chemfinder SMP CHS amet 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 ametam S-Adenosylmethioninamine C14H24N6O3S 2 C01137 KEGG - C01137 SMP Changed according to Genomatica JLR amob S-Adenosyl-4-methylthio-2-oxobutanoate C15H19N5O6S 0 C04425 KEGG - C04425 Neutral MF = C15H20N5O6S SMP CHS Checked N-groups JLR amp AMP C10H12N5O7P -2 61-19-8 C00020 KEGG - C00020 Neutral MF = C10H14N5O7P SMP CHS anhgm N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid C19H29N2O12 -1 AMF anhgm3p N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide C34H52N6O19 -2 AMF anhgm4p N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide C37H57N7O20 -2 AMF anhm 1,6-anhydrous-N-Acetylmuramate C11H16NO7 -1 AMF anhm3p 1,6-anhydrous-N-Acetylmuramyl-tripeptide C26H39N5O14 -2 AMF anhm4p 1,6-anhydrous-N-Acetylmuramyl-tetrapeptide C29H44N6O15 -2 AMF anth Anthranilate C7H6NO2 -1 118-92-3 C00108 KEGG - C00108 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR ap4a P1,P4-Bis(5'-adenosyl) tetraphosphate C20H24N10O19P4 -4 C01260 Kegg- C01260 Neutral-C20H28N10O19P4 JLR ap5a P1,P5-Bis(5'-adenosyl) pentaphosphate C20H24N10O22P5 -5 4637-56-3 C04058 KEGG - C04058 Neutral-C20H29N10O22P5 JLR apg_EC acyl phosphatidylglycerol (E.coli) C2829H5272O550P50 -50 acyl group is attached to the second glycerol molecule Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 apg_EC is really one molecule of apg. JLR apoACP apoprotein [acyl carrier protein] RHO 0 JLR aps Adenosine 5'-phosphosulfate C10H12N5O10PS -2 C00224 KEGG - C00224 Neutral MF = C10H14N5O10PS SMP CHS Checked N-groups JLR ara5p D-Arabinose 5-phosphate C5H9O8P -2 C01112 KEGG - C01112 neutral MF = C5H11O8P SMP CHS JLR- had incorrect charge should be -2 arab-L L-Arabinose C5H10O5 0 147-81-9 C00259 KEGG - C00259 Neutral Compound SMP CHS aragund O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C71H115N1O17P2 -2 AMF arbt6p Arbutin 6-phosphate C12H15O10P -2 C06187 KEGG - C06187 Neutral MF = C12H17O10P SMP arbtn aerobactin minus Fe3 C22H33N4O13 -3 0 arbtn-fe3 Aerobactin C22H33FeN4O13 0 61-33-6 C05554 KEGG - C05554 AMF is a siderophore - Fe-scavenging molecule. requires secretion and re-uptake pathways arg-L L-Arginine C6H15N4O2 1 74-79-3 C00062 KEGG - C00062 Neutral MF = C6H14N4O2 SMP CHS Changed according to Genomatica JLR argsuc 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 argtrna L-Arginyl-tRNA(Arg) C6H14N4OR 2 C02163 KEGG - C02163 SMP adjusted for Genomatica's change to aa - NCD ascb6p L-ascorbate-6-phosphate C6H7O9P -2 No Kegg Entry JLR ascb-L L-Ascorbate C6H8O6 0 50-81-7 C00072 KEGG - C00072 JLR asn-L L-Asparagine C4H8N2O3 0 70-47-3 C00152 KEGG - C00152 Neutral MF = C4H8N2O3 SMP CHS Changed according to Genomatica JLR asntrna L-Asparaginyl-tRNA(Asn) C4H7N2O2R 1 C03402 KEGG - C03402 SMP adjusted for Genomatica's change to aa - NCD aso3 arsenite AsO3 -3 C06697 KEGG - C06697 AMF aso4 arsenate AsO4 -3 7778-39-4 C01478 KEGG - C01478 AMF asp-L L-Aspartate C4H6NO4 -1 56-84-8 C00049 KEGG - C00049 Neutral MF = C4H7NO4 SMP CHS Changed according to Genomatica JLR aspsa L-Aspartate 4-semialdehyde C4H7NO3 0 None C00441 KEGG - C00441 Neutral MF = C4H7NO3 SMP CHS Changed according to Genomatica JLR asptrna L-Aspartyl-tRNA(Asp) C4H5NO3R 0 C02984 KEGG - C02984 SMP athr-L L-Allo-threonine C4H9NO3 0 28954-12-3 C05519 KEGG - C05519 AMF atp ATP C10H12N5O13P3 -4 56-65-5 C00002 KEGG - C00002 Neutral MF = C10H16N5O13P3 SMP CHS b2coa trans-But-2-enoyl-CoA C25H36N7O17P3S -4 102680-35-3 C00877 KEGG - C00877 Neutral MF = C25H40N7O17P3S SMP bbtcoa 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 betald Betaine aldehyde C5H12NO 1 C00576 KEGG - C00576 JLR Checked N-groups JLR bglycogen branching glycogen C6H10O5 0 AMF btal Butanal C4H8O 0 123-72-8 C01412 KEGG - C01412 Neutral Compound SMP btcoa Butanoyl-CoA C25H38N7O17P3S -4 C00136 KEGG - C00136 Neutral MF = C25H42N7O17P3S SMP btn Biotin C10H15N2O3S -1 58-85-5 C00120 KEGG - C00120 Neutral MF = C10H16N2O3S SMP CHS Checked N-groups JLR btnso d-biotin d-sulfoxide C10H15N2O4S -1 Not in Kegg (see PMID 10747793, figure 1) Neutral- C10H16N2O4S JLR Checked N-groups JLR but Butyrate (n-C4:0) C4H7O2 -1 107-92-6 C00246 KEGG - C00246 Neutral MF = C4H8O2 SMP changed compound class from peptides - NCD butso3 butanesulfonate C4H9O3S -1 AMF camp cAMP C10H11N5O6P -1 C00575 Kegg C00575 Neutral-C10H12N5O6P JLR cbasp N-Carbamoyl-L-aspartate C5H6N2O5 -2 C00438 KEGG - C00438 Neutral MF = C5H8N2O5 SMP CHS Checked N-groups JLR cbi 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) cbl1 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) cbp Carbamoyl phosphate CH2NO5P -2 C00169 KEGG - C00169 Neutral MF = CH4NO5P SMP CHS Checked N-groups JLR cd2 Cadmium Cd 2 C01413 KEGG - C01413 SMP (02/16/03) cdp CDP C9H12N3O11P2 -3 63-38-7 C00112 KEGG - C00112 Neutral MF = C9H15N3O11P2 SMP CHS cdpdag_EC CDPdiacylglycerol (E coli) C2286H3998N150O750P100 -100 C00269 scaled up (50x) of CDP diacylglycerol with 2 ave fatty acids should be charge of -100 cdpea CDPethanolamine C11H19N4O11P2 -1 C00570 KEGG - C00570 Neutral MF = C11H20N4O11P2 SMP CHS Checked N-groups JLR cechddd cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol C9H11O4 -1 No Kegg entry, see figure 1 PMID: 9603882 Neutral-C9H12O4 JLR cenchddd cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol C9H9O4 -1 No KEGG entry see Figure 1in PMID: 9603882 Neutral-C9H10O4 JLR chol Choline C5H14NO 1 62-49-7 C00114 KEGG - C00114 SMP Checked N-groups JLR chor chorismate C10H8O6 -2 55508-12-8 C00251 KEGG - C00251 Neutral MF = C10H10O6 SMP CHS cinnm trans-Cinnamate C9H7O2 -1 140-10-3 C00423 KEGG - C00423 Neutral-C9H8O2 JLR cit Citrate C6H5O7 -3 77-92-9 C00158 KEGG - C00158 Neutral MF = C6H8O7 SMP CHS citr-L L-Citrulline C6H13N3O3 0 372-75-8 C00327 KEGG - C00327 Neutral MF = C6H13N3O3 SMP CHS Changed according to Genomatica JLR ckdo CMP-3-deoxy-D-manno-octulosonate C17H24N3O15P -2 JLR- like KEGG C04121 except ring structure (see NH page 1044) cl Chloride Cl -1 C00115 0 clpn_EC Cardiolipin (Ecoli) C3822H7096O850P100 -100 C05980 KEGG - C05980 JLR- really represents 50 cardiolipin molecules, based on composition of fatty acids in E.coli (0.04 C14:0, 0.1 C14:1, 0.72 C16:0, 0.14 C16:1, 1.0 C18:1) cmp CMP C9H12N3O8P -2 84-52-6 C00055 KEGG - C00055 Neutral MF = C9H14N3O8P SMP CHS co2 CO2 CO2 0 124-38-9 C00011 KEGG - C00011 Neutral Compound SMP CHS coa 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 cobalt2 Co2+ Co 2 7440-48-4 C00175 KEGG - C00175 colipa core oligosaccharide lipid A C176H303N2O100P4 -11 AMF cpe_EC Phosphatidylethanolamine (ecoli) C1986H3848N50O400P50 0 AMF org: Hpylori, Ecoli scaled up (50x) of ps with 2 ave fatty acids cpg_EC cyclopropane phosphatidylglycerol (Ecoli) C2036H3848O500P50 -50 tv org: Ecoli scaled up (50x) of phosphatidylglycerol with an ave fatty acid of C1686 H3148 O100 cpgn coprogen C35H52N6O13Fe -1 AMF cpgn-un coprogen unloaded (no Fe(III)) C35H52N6O13 -4 AMF cpppg3 Coproporphyrinogen III C36H40N4O8 -4 2624-63-7 C03263 KEGG - C03263 Deleted C02667 (Coproporphyrinogen) Neutral MF = C36H44N4O8 SMP CHS Checked N-groups JLR crn 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 crncoa 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 crn-D D-Carnitine C7H15NO3 0 C00487 KEGG - C00487 AMF crnDcoa D-carnitinyl-CoA C28H46N8O18P3S -3 AMF csn Cytosine C4H5N3O 0 71-30-7 C00380 KEGG - C00380 Neutral Compound SMP CHS ctbt 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 ctbtcoa 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 ctp CTP C9H12N3O14P3 -4 65-47-4 C00063 KEGG - C00063 Neutral MF = C9H16N3O14P3 SMP CHS cu Cu+ Cu 1 C00070 cu2 Cu2+ Cu 2 Two entries are made for Cu: Cu3+ and Cu2+ cyan Hydrogen cyanide CHN 0 57-12-5 C01326 KEGG - C01326 JLR pKa of H attached to C is 9.3 Checked N-groups JLR cynt Cyanate CNO -1 420-05-3 C01417 KEGG - C01417 Neutral-CHNO JLR Checked N-groups JLR cys-D D-Cysteine C3H7NO2S 0 921-01-7 C00793 KEGG - C00793 JLR Changed according to Genomatica JLR cys-L L-Cysteine C3H7NO2S 0 52-90-4 C00097 KEGG - C00097 Neutral MF = C3H7NO2S SMP CHS Changed according to Genomatica JLR cyst-L L-Cystathionine C7H14N2O4S 0 56-88-2 C02291 KEGG - C02291 Neutral MF = C7H14N2O4S SMP CHS Changed according to Genomatica JLR cystrna L-Cysteinyl-tRNA(Cys) C3H6NOSR 1 C03125 KEGG - C03125 SMP adjusted for Genomatica's change to aa - NCD cytd Cytidine C9H13N3O5 0 65-46-3 C00475 KEGG - C00475 Neutral Compound SMP CHS Checked N-groups JLR dad-2 Deoxyadenosine C10H13N5O3 0 958-09-8 C00559 KEGG - C00559 Neutral Compound SMP CHS Checked N-groups JLR dad-5 5'-Deoxyadenosine C10H13N5O3 0 C05198 KEGG - C05198 Neutral Compound SMP CHS dadp dADP C10H12N5O9P2 -3 None C00206 KEGG - C00206 Neutral MF = C10H15N5O9P2 SMP CHS damp dAMP C10H12N5O6P -2 653-63-4 C00360 KEGG - C00360 Neutral MF = C10H14N5O6P SMP CHS dann 7,8-Diaminononanoate C9H21N2O2 1 C01037 KEGG - C01037 Neutral MF = C9H20N2O2 SMP CHS Changed according to Genomatica JLR datp dATP C10H12N5O12P3 -4 1927-31-7 C00131 KEGG - C00131 Neutral MF = C10H16N5O12P3 SMP CHS db4p 3,4-dihydroxy-2-butanone 4-phosphate C4H7O6P -2 No KEGG Entry Neutral MF = C4H9O6P SMP dc2coa trans-Dec-2-enoyl-CoA C31H48N7O17P3S -4 C05275 KEGG - C05275 Neutral MF = C31H52N7O17P3S SMP dca 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 dcacoa Decanoyl-CoA (n-C10:0CoA) C31H50N7O17P3S -4 C05274 KEGG - C05274 Neutral MF = C31H54N7O17P3S SMP dcamp N6-(1,2-Dicarboxyethyl)-AMP C14H14N5O11P -4 C03794 KEGG - C03794 Neutral MF = C14H18N5O11P SMP CHS Checked N-groups JLR dcdp dCDP C9H12N3O10P2 -3 None C00705 KEGG - C00705 Neutral MF = C9H15N3O10P2 SMP CHS dcmp dCMP C9H12N3O7P -2 1032-65-1 C00239 KEGG - C00239 Neutral MF = C9H14N3O7P SMP CHS dctp dCTP C9H12N3O13P3 -4 2056-98-6 C00458 KEGG - C00458 Neutral MF = C9H16N3O13P3 SMP CHS dcyt Deoxycytidine C9H13N3O4 0 951-77-9 C00881 KEGG - C00881 Neutral Compound SMP CHS Checked N-groups JLR dd2coa trans-Dodec-2-enoyl-CoA C33H52N7O17P3S -4 C03221 KEGG - C03221 Neutral MF = C33H56N7O17P3S SMP ddca 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 ddcaACP Dodecanoyl-ACP (n-C12:0ACP) C23H43N2O8PRS -1 C05223 KEGG C05223 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) ddcacoa Dodecanoyl-CoA (n-C12:0CoA) C33H54N7O17P3S -4 6244-92-4 C01832 KEGG - C01832 Neutral MF = C33H58N7O17P3S SMP dgdp dGDP C10H12N5O10P2 -3 C00361 KEGG - C00361 Neutral MF=C10H15N5O10P2 CHS dgmp dGMP C10H12N5O7P -2 902-04-5 C00362 KEGG - C00362 Neutral MF = C10H14N5O7P SMP CHS dgsn Deoxyguanosine C10H13N5O4 0 961-07-9 C00330 KEGG - C00330 Neutral Compound SMP CHS Checked N-groups JLR dgtp dGTP C10H12N5O13P3 -4 2564-35-4 C00286 KEGG - C00286 Neutral MF = C10H16N5O13P3 SMP CHS dha Dihydroxyacetone C3H6O3 0 96-26-4 C00184 KEGG - C00184 dhap Dihydroxyacetone phosphate C3H5O6P -2 57-04-5 C00111 KEGG - C00111 Neutral MF = C3H7O6P SMP CHS dhcinnm 2,3-dihydroxicinnamic acid C9H7O4 -1 No Kegg entry see figure 1 PMID: 9603882 Neutral-C9H8O4 JLR dhf 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 dhmptp dihydromonapterin-triphosphate C9H12N5O13P3 -4 AMF dhna 1,4-Dihydroxy-2-naphthoate C11H7O4 -1 C03657 KEGG - C03657 Neutral MF = C11H8O4 SMP CHS dhnpt 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 dhor-S (S)-Dihydroorotate C5H5N2O4 -1 5988-19-2 C00337 KEGG - C00337 Neutral MF = C5H6N2O4 SMP Checked N-groups JLR dhpmp 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 dhpppn 3-(2,3-Dihydroxyphenyl)propanoate C9H9O4 -1 145-14-2 C04044 KEGG - C04044 Neutral-C9H10O4 JLR dhpt Dihydropteroate C14H13N6O3 -1 C00921 KEGG - C00921 Neutral MF = C14H14N6O3 SMP CHS Checked N-groups, agrees with ACD software JLR dhptd 4,5-dihydroxy-2,3-pentanedione C5H8O4 0 C11838 KEGG C11838 See PMID: 11489131 JLR dimp dIMP C10H11N4O7P -2 C06196 KEGG - C06196 (figure in Kegg is inconsistent with other inosine bases) IT Neutral MF = C10H15N4O7P SMP CHS din Deoxyinosine C10H12N4O4 0 890-38-0 C05512 KEGG - C05512 Neutral Compound SMP CHS Checked N-groups JLR ditp dITP C10H11N4O13P3 -4 66701-25-5 C01345 KEGG - C01345 Neutral MF = C10H15N4O13P3 SMP CHS dkmpp 2,3-diketo-5-methylthio-1-phosphopentane C6H9O6PS -2 JLR- no kegg entry dmbzid 5,6-Dimethylbenzimidazole C9H10N2 0 582-60-5 C03114 KEGG - C03114 SMP JLR Checked N-groups JLR dmlz 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 dmpp Dimethylallyl diphosphate C5H9O7P2 -3 358-71-4 C00235 KEGG - C00235 Neutral MF = C5H12O7P2 SMP CHS dms Dimethyl sulfide C2H6S 0 75-18-3 C00580 KEGG - C00580 dmso Dimethyl sulfoxide C2H6OS 0 C11143 KEGG C11143 JLR dnad Deamino-NAD+ C21H24N6O15P2 -2 C00857 KEGG - C00857 Neutral MF = C21H27N6O15P2 SMP Checked N-groups JLR dopa Dopamine C8H12NO2 1 51-61-6 C03758 KEGG - C03758 SAB dpcoa Dephospho-CoA C21H33N7O13P2S -2 C00882 KEGG - C00882 Neutral MF = C21H35N7O13P2S SMP CHS Checked N-groups JLR dscl dihydrosirohydrochlorin C42H41N4O16 -7 65207-12-7 C02463 KEGG - C02463 Neutral MF = C42H48N4O16 SMP Checked N-groups, agrees with ACD software, JLR dtbt Dethiobiotin C10H17N2O3 -1 C01909 KEGG - C01909 Neutral MF = C10H18N2O3 SMP CHS Checked N-groups JLR dtdp dTDP C10H13N2O11P2 -3 C00363 KEGG - C00363 Neutral MF = C10H16N2O11P2 SMP CHS dtdp4aaddg 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 dtdp4addg dTDP-4-amino-4,6-dideoxy-D-glucose C16H26N3O14P2 -1 157296-99-6 C04268 KEGG - C04268 Neutral-C16H25N3O14P2 JLR Checked N-groups JLR dtdp4d6dg dTDP-4-dehydro-6-deoxy-D-glucose C16H22N2O15P2 -2 C00687 KEGG - C00687 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR dtdp4d6dm dTDP-4-dehydro-6-deoxy-L-mannose C16H22N2O15P2 -2 C00688 KEGG - C00688 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR dtdpglu dTDPglucose C16H24N2O16P2 -2 2009-24-7 C00842 KEGG - C00842 Neutral-C16H26N2O16P2 JLR Checked N-groups JLR dtdprmn dTDP-L-rhamnose C16H24N2O15P2 -2 572-96-3 C03319 KEGG - C03319 Neutral-C16H26N2O15P2 JLR Checked N-groups JLR dtmp dTMP C10H13N2O8P -2 365-07-1 C00364 KEGG - C00364 Neutral MF = C10H15N2O8P Thymine is normally found as a deoxyriboside SMP CHS dttp dTTP C10H13N2O14P3 -4 C00459 KEGG - C00459 Neutral MF = C10H17N2O14P3 SMP CHS dudp dUDP C9H11N2O11P2 -3 C01346 KEGG - C01346 Neutral MF = C9H14N2O11P2 SMP CHS dump dUMP C9H11N2O8P -2 964-26-1 C00365 KEGG - C00365 Neutral MF = C9H13N2O8P SMP CHS duri Deoxyuridine C9H12N2O5 0 951-78-0 C00526 KEGG - C00526 Neutral Compound SMP CHS Checked N-groups JLR dutp dUTP C9H11N2O14P3 -4 C00460 KEGG - C00460 Neutral MF = C9H15N2O14P3 SMP CHS dxyl 1-deoxy-D-xylulose C5H10O4 0 C06257 KEGG C06257 tv Neidhardt pg 683 dxyl5p 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 e4p D-Erythrose 4-phosphate C4H7O7P -2 585-18-2 C00279 KEGG - C00279 Neutral MF = C4H9O7P SMP CHS eca2und (enterobacterial common antigen)x2 undecaprenyl-diphosphate C103H162N6O37P2 -4 AMF eca3und (enterobacterial common antigen)x3 undecaprenyl-diphosphate C127H198N9O52P2 -5 AMF eca4colipa (enterobacterial common antigen)x4 core oligosaccharide lipid A C272H447N14O160P4 -15 AMF eca4und (enterobacterial common antigen)x3 undecaprenyl-diphosphate C151H234N12O67P2 -6 AMF eig3p D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate C6H9N2O6P -2 C04666 KEGG - C04666 Neutral MF = C6H11N2O6P SMP CHS Checked N-groups JLR enlipa phosphoethanolamine KDO(2)-lipid (A) C112H202N3O42P3 -6 AMF enter 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 etha Ethanolamine C2H8NO 1 141-43-5 C00189 KEGG - C00189 Checked N-groups JLR ethso3 ethanesulfonate C2H5O3S -1 AMF etoh Ethanol C2H6O 0 64-17-5 C00469 KEGG - C00469 Neutral Compound SMP CHS f1p D-Fructose 1-phosphate C6H11O9P -2 15978-08-2 C02976 KEGG - C02976 Merged with KEGG - C01094 Neutral MF = C6H13O9P SMP CHS f6p D-Fructose 6-phosphate C6H11O9P -2 643-13-0 C00085 KEGG - C00085 Neutral MF = C6H13O9P SMP CHS fad 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 fadh2 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 fald Formaldehyde CH2O 0 50-00-0 C00067 KEGG - C00067 Neutral Compound SMP CHS fc1p 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 fcl-L 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 fdp D-Fructose 1,6-bisphosphate C6H10O12P2 -4 488-69-7 C00354 KEGG - C00354 Neutral MF = C6H14O12P2 SMP CHS fe2 Fe2+ Fe 2 None C00023 KEGG - C00023 Neutral Compound SMP CHS fe3 Fe3+ Fe 3 None Neutral Compound SMP CHS fe3dcit Fe(III)dicitrate C12H10FeO14 -3 90-02-8 C06229 KEGG - C06229 AMF- not sure if any h complexed with iron or carboxyls fe3dhbzs ferric 2,3-dihydroxybenzoylserine C10H10NO6Fe 2 AMF fe3hox Fe(III)hydroxamate C9H18O6N3Fe 0 C06227 KEGG - C06227 formula corrected, 3/24/05 MKA contains R groups - replaced with ethyl groups fe3hox-un 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 fecrm Ferrichrome C27H42FeN9O12 0 90-02-8 C06228 KEGG - C06228 AMF CHEMID (015630645) fecrm-un Ferrichrome minus Fe(III) C27H42N9O12 -3 CHEMID (015630645) feenter Fe-enterobactin C30H27FeN3O15 3 90-02-8 C06230 KEGG - C06230 feoxam ferroxamine C25H46FeN6O8 1 C07597 AMF feoxam-un ferroxamine minus Fe(3) C25H46N6O8 -2 siderophore fgam N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide C8H13N2O9P -2 C04376 KEGG - C04376 Neutral MF = C8H15N2O9P SMP CHS Checked N-groups JLR fldox flavodoxin (oxidized) X 0 121-69-7 C02869 KEGG - C02869 fldrd flavodoxin (reduced) XH2 0 358-71-4 C02745 KEGG - C02745 fmettrna N-Formylmethionyl-tRNA C6H9NO2SR 0 C03294 KEGG - C03294 SMP fmn 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 fmnh2 Reduced FMN C17H21N4O9P -2 67-63-0 KEGG - C01847 Neutral-C17H23N4O9P JLR for Formate CH1O2 -1 64-18-6 C00058 KEGG - C00058 Neutral MF = CH2O2 SMP CHS fpram 2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine C8H15N3O8P -1 C04640 KEGG - C04640 Neutral MF = C8H16N3O8P SMP CHS Changed according to Genomatica JLR fprica 5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide C10H13N4O9P -2 C04734 KEGG - C04734 Neutral MF = C10H15N4O9P SMP Checked N-groups JLR frdp Farnesyl diphosphate C15H25O7P2 -3 13058-04-3 C00448 KEGG - C00448 Neutral MF = C15H28O7P2 SMP fru D-Fructose C6H12O6 0 57-48-7 C00095 KEGG - C00095 Deleted KEGG -C01496 (fructose) Neutral Compound SMP CHS frulys fructoselysine C12H25N2O7 1 MKA frulysp fructoselysine Phosphate C12H24N2O10P -1 MKA AMF fruur D-Fructuronate C6H9O7 -1 669-90-9 C00905 KEGG - C00905 Neutral MF = C6H10O7 SMP CHS fuc1p-L L-Fucose 1-phosphate C6H11O8P -2 526-31-8 C02985 KEGG - C02985 Neutral-C6H13O8P JLR fuc-L L-Fucose C6H12O5 0 2438-80-4 C01019 KEGG - C01019 Neutral Compound SMP fum Fumarate C4H2O4 -2 110-17-8 C00122 KEGG - C00122 Neutral MF = C4H4O4 SMP CHS g1p D-Glucose 1-phosphate C6H11O9P -2 59-56-3 C00103 KEGG - C00103 Neutral MF = C6H13O9P SMP CHS g3p 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) g3pc sn-Glycero-3-phosphocholine C8H20NO6P 0 C00670 KEGG - C00670 Normally has a + charge (C8H21NO6P) JLR g3pe sn-Glycero-3-phosphoethanolamine C5H14NO6P 0 C01233 KEGG - C01233 Neutral-C5H14NO6P JLR Checked N JLR g3pg Glycerophosphoglycerol C6H14O8P -1 11034-93-8 C03274 KEGG - C03274 Neutral-C6H15O8P JLR g3pi sn-Glycero-3-phospho-1-inositol C9H18O11P -1 C01225 KEGG - C01225 Neutral-C9H19O11P JLR g3ps Glycerophosphoserine C6H13NO8P -1 No Kegg entry Neutral-C6H14NO8P JLR Checked N JLR g6p D-Glucose 6-phosphate C6H11O9P -2 56-73-5 C00092 KEGG - C00092 Neutral MF = C6H13O9P SMP CHS gagicolipa galactosyl-glucosyl-inner core oligosaccharide lipid A C157H271N2O84P4 -11 AMF gal D-Galactose C6H12O6 0 59-23-4 C00124 KEGG - C00124 Deleted KEGG - C01582 (Galactose) Neutral Compound SMP CHS gal1p alpha-D-Galactose 1-phosphate C6H11O9P -2 2255-14-3 C00446 KEGG - C00446 Neutral MF = C6H13O9P SMP CHS gal-bD beta D-Galactose C6H12O6 0 33419-42-0 C01582 KEGG - C01582 NCD galct-D D-Galactarate C6H8O8 -2 526-99-8 C00879 KEGG - C00879 Neutral-C6H10O8 JLR galctn-D D-Galactonate C6H11O7 -1 C00880 KEGG - C00880 Neutral-C6H12O7 JLR galt Galactitol C6H14O6 0 608-66-2 C01697 KEGG - C01697 Neutral Compound SMP galt1p Galactitol 1-phosphate C6H13O9P -2 C06311 KEGG- C06311 Neutral MF = C6H15O9P JLR galur D-Galacturonate C6H9O7 -1 685-73-4 C00333 KEGG - C00333 Neutral MF = C6H10O7 SMP CHS gam D-Glucosamine C6H14NO5 1 3416-24-8 C00329 KEGG - C00329 Neutral Compound SMP CHS Changed according to Genomatica JLR gam1p D-Glucosamine 1-phosphate C6H13NO8P -1 C06156 KEGG - C06156 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR gam6p D-Glucosamine 6-phosphate C6H13NO8P -1 3616-42-0 C00352 KEGG - C00352 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR gar N1-(5-Phospho-D-ribosyl)glycinamide C7H14N2O8P -1 C03838 KEGG - C03838 Neutral MF = C7H15N2O8P SMP CHS Changed according to Genomatica JLR garagund glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C77H125N1O22P2 -2 AMF gbbtn 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 gcald Glycolaldehyde C2H4O2 0 C00266 KEGG - C00266 SMP CHS gdp GDP C10H12N5O11P2 -3 146-91-8 C00035 KEGG - C00035 Neutral MF = C10H15N5O11P2 SMP CHS gdpddman GDP-4-dehydro-6-deoxy-D-mannose C16H21N5O15P2 -2 C01222 KEGG - C01222 Neutral: C16H23N5O15P2 JLR Checked N-groups JLR gdpfuc GDP-L-fucose C16H23N5O15P2 -2 C00325 KEGG - C00325 KEGG glycan: G10615 Neutral: C16H25N5O15P2 JLR gdpmann GDP-D-mannose C16H23N5O16P2 -2 C00096 KEGG C00096 Neutral:C16H25N5O16P2 JLR Checked N-groups JLR gdpofuc GDP-4-oxo-L-fucose C16H21N5O15P2 -2 583-08-4 C05389 KEGG - C05389 Neutral: C16H23N5O15P2 JLR Checked N-Groups JLR gdptp Guanosine 3'-diphosphate 5'-triphosphate C10H11N5O20P5 -7 C04494 KEGG - C04494 Neutral MF = C10H18N5O20P5 SMP CHS gfgaragund galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C83H135N1O27P2 -2 AMF gg4abut gamma-glutamyl-gamma aminobutyric acid C9H15O5N2 -1 MKA ggagicolipa glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C163H281N2O89P4 -11 AMF ggbutal gamma-glutamyl-gamma-butyraldehyde C9H16O4N2 0 MKA gggagicolipa glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C169H291N2O94P4 -11 AMF ggptrc gamma-glutamyl-putrescine C9H20O3N3 1 MKA AMF gicolipa glucosyl-inner core oligosaccharide lipid A C151H261N2O79P4 -11 AMF glc-D 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 glcn D-Gluconate C6H11O7 -1 526-95-4 C00257 KEGG - C00257 Neutral MF = C6H12O7 SMP CHS glcr D-Glucarate C6H8O8 -2 87-73-0 C00818 KEGG - C00818 KEGG - C00767 has Glucarate is deleted from the database Neutral MF = C6H10O8 SMP CHS glcur D-Glucuronate C6H9O7 -1 12/03/6556 C00191 KEGG - C00191 Neutral MF = C6H10O7 SMP CHS glcur1p D-Glucuronate 1-phosphate C6H8O10P -3 583-08-4 C05385 KEGG - C05385 NCD gln-L L-Glutamine C5H10N2O3 0 56-85-9 C00064 KEGG - C00064 Neutral MF = C5H10N2O3 SMP CHS glntrna L-Glutaminyl-tRNA(Gln) C5H9N2O2R 1 C02282 KEGG - C02282 SMP adjusted for Genomatica's change to aa - NCD glu1sa L-Glutamate 1-semialdehyde C5H9NO3 0 None C03741 KEGG - C03741 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR glu5p L-Glutamate 5-phosphate C5H8NO7P -2 C03287 KEGG - C03287 Neutral MF = C5H10NO7P SMP Changed according to Genomatica JLR glu5sa L-Glutamate 5-semialdehyde C5H9NO3 0 None C01165 KEGG - C01165 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR glucys gamma-L-Glutamyl-L-cysteine C8H13N2O5S -1 686-58-8 C00669 KEGG - C00669 Neutral MF = C8H14N2O5S SMP CHS Changed according to Genomatica JLR glu-D D-Glutamate C5H8NO4 -1 56-86-0 C00217 KEGG - C00217 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR glu-L L-Glutamate C5H8NO4 -1 56-86-0 C00025 KEGG - C00025 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR glutrna 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 glx Glyoxylate C2H1O3 -1 298-12-4 C00048 KEGG - C00048 Neutral MF = C2H2O3 SMP CHS gly Glycine C2H5NO2 0 56-40-6 C00037 KEGG - C00037 Nonchiral compound Neutral MF = C2H5NO2 SMP CHS Changed according to Genomatica JLR glyald D-Glyceraldehyde C3H6O3 0 453-17-8 C00577 KEGG - C00577 KEGG has non-chiral glyceraldehyde (367-47-5) Neutral Compound SMP CHS glyb Glycine betaine C5H11NO2 0 107-43-7 C00719 KEGG - C00719 SMP Checked N-groups JLR glyc Glycerol C3H8O3 0 56-81-5 C00116 KEGG - C00116 Neutral Compound SMP CHS glyc2p Glycerol 2-phosphate C3H7O6P -2 3249-68-1 C02979 KEGG - C02979 AMF glyc3p Glycerol 3-phosphate C3H7O6P -2 C00093 KEGG - C00093 Neutral MF = C3H9O6P SMP glyclt Glycolate C2H3O3 -1 79-14-1 C00160 KEGG - C00160 Neutral MF = C2H4O3 SMP CHS glycogen glycogen C6H10O5 0 C00182 KEGG- C00182 MF revised on May-7-2002 Deleted previous entry glcgn Polymer with unit MF = C6H10O5 SMP glyc-R (R)-Glycerate C3H5O4 -1 473-81-4 C00258 KEGG - C00258 Neutral MF = C3H6O4 SMP CHS glytrna Glycyl-tRNA(Gly) C2H4NOR 1 C02412 KEGG - C02412 SMP adjusted for Genomatica's change to aa - NCD gmhep17bp D-Glycero-D-manno-heptose 1,7-bisphosphate C7H12O13P2 -4 C11472 Kegg C11472 Neutral- C7H16O13P2 JLR gmhep1p D-Glycero-D-manno-heptose 1-phosphate C7H13O10P -2 C07838 KEGG C07838 Neutral C7H15O10P gmhep7p D-Glycero-D-manno-heptose 7-phosphate C7H13O10P -2 C07836 Kegg C07836 Neutral-C7H15O10P JLR gmp GMP C10H12N5O8P -2 85-32-5 C00144 KEGG - C00144 Neutral = C10H14N5O8P SMP CHS gp4g P1,P4-Bis(5'-guanosyl) tetraphosphate C20H24N10O21P4 -4 C01261 Kegg- C01261 Neutral-C20H28N10O21P4 JLR grdp Geranyl diphosphate C10H17O7P2 -3 C00341 KEGG - C00341 Neutral MF = C10H20O7P2 SMP grxox glutaredoxin (oxidized) X 0 AMf C07293 grxrd glutaredoxin (reduced) XH2 0 AMF C07292 gsn Guanosine C10H13N5O5 0 118-00-3 C00387 KEGG - C00387 Neutral Compound SMP CHS Checked N-groups JLR gthox Oxidized glutathione C20H30N6O12S2 -2 C00127 KEGG - C00127 Neutral MF = C20H32N6O12S2 SMP CHS Changed according to Genomatica JLR gthrd Reduced glutathione C10H16N3O6S -1 70-18-8 C00051 KEGG - C00051 Neutral MF = C10H17N3O6S SMP CHS Changed according to Genomatica JLR gtp GTP C10H12N5O14P3 -4 86-01-1 C00044 KEGG - C00044 Neutral MF = C10H16N5O14P3 SMP CHS gtspmd Glutathionylspermidine C17H36N6O5S 2 08/06/7783 C05730 KEGG - C05730 Neutral-C17H34N6O5S JLR Checked N-groups JLR gua Guanine C5H5N5O 0 73-40-5 C00242 KEGG - C00242 Neutral Compound SMP CHS h H+ H 1 12408-02-5 C00080 KEGG - C00080 h2 H2 H2 0 1333-74-0 C00282 KEGG - C00282 h2mb4p 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate C5H9O8P2 -3 C11811 KEGG C11811 JLR see PMID 12010124 h2o H2O H2O 0 7732-18-5 C00001 KEGG - C00001 h2o2 Hydrogen peroxide H2O2 0 7722-84-1 C00027 KEGG - C00027 Neutral Compound SMP CHS h2s Hydrogen sulfide H2S 0 06/04/7783 C00283 KEGG - C00283 Neutral Compound SMP CHS hacolipa hepta-acylated core oligosaccharide lipid A (E. coli) C192H333N2O101P4 -11 AMF halipa hepta-acylated KDO(2)-lipid (A) C126H226N2O40P2 -6 AMF hco3 Bicarbonate CHO3 -1 71-52-3 C00288 KEGG - C00288 SMP CHS hcys-L L-Homocysteine C4H9NO2S 0 6027-13-0 C00155 KEGG - C00155 Deleted C05330 Neutral MF = C4H9NO2S SMP CHS Changed according to Genomatica JLR hdca 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 hdcea 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 hdd2coa trans-Hexadec-2-enoyl-CoA C37H60N7O17P3S -4 C05272 KEGG - C05272 Neutral MF = C37H64N7O17P3S SMP 1 degree of unsaturation hdeACP Hexadecenoyl-ACP (n-C16:1ACP) C27H49N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) hemeO Heme O C49H56FeN4O5 -2 No KEGG Entry Neutral MF = C49H58FeN4O5 SMP Note Neidhardt picture (pg 734) is incorrect Checked N-groups, JLR hg2 Hg2+ Hg 2 C00703 KEGG - C00703 hhlipa heptosyl-heptosyl-kdo2-lipidA C124H220N2O51P2 -6 AMF his-L L-Histidine C6H9N3O2 0 71-00-1 C00135 KEGG - C00135 Neutral MF = C6H9N3O2 SMP CHS Changed according to Genomatica JLR hisp L-Histidinol phosphate C6H11N3O4P -1 25679-93-0 C01100 KEGG - C01100 Neutral MF = C6H12N3O4P SMP CHS Changed according to Genomatica JLR histd L-Histidinol C6H12N3O 1 None C00860 KEGG - C00860 Neutral Compound SMP CHS Changed according to Genomatica JLR histrna L-Histidyl-tRNA(His) C6H8N3OR 1 C02988 KEGG - C02988 SMP adjusted for Genomatica's change to aa - NCD hkndd 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 hkntd 2-hydroxy-6-ketononatrienedioate C9H6O6 -2 No Kegg entry, see PMID: 9603882 Neutral- C9H8O6 JLR Changed to -2 charge hlipa heptosyl-kdo2-lipidA C117H208N2O45P2 -6 AMF hmbil Hydroxymethylbilane C40H38N4O17 -8 73023-76-4 C01024 KEGG - C01024 Neutral MF = C40H46N4O17 SMP CHS Checked N-groups JLR hmfurn 4-hydroxy-5-methyl-3(2H)-furanone C5H6O3 0 No Kegg Entry See PMID: 11489131 JLR hmgth hydroxymethylglutathione C11H18N3O7S -1 AMF hom-L L-Homoserine C4H9NO3 0 672-15-1 C00263 KEGG - C00263 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR hphhlipa heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H231N2O60P3 -8 AMF hpyr Hydroxypyruvate C3H3O4 -1 1113-60-6 C00168 KEGG - C00168 Neutral MF = C3H4O4 SMP CHS hqn Hydroquinone C6H6O2 0 123-31-9 C00530 KEGG - C00530 SMP hx2coa trans-Hex-2-enoyl-CoA C27H40N7O17P3S -4 C05271 KEGG - C05271 Neutral MF = C27H44N7O17P3S SMP hxa Hexanoate (n-C6:0) C6H11O2 -1 142-62-1 C01585 KEGG - C01585 Neutral MF = C6H12O2 SMP changed compound class from peptides - NCD hxan Hypoxanthine C5H4N4O 0 68-94-0 C00262 KEGG - C00262 Neutral Compound SMP CHS Checked N-groups JLR hxcoa Hexanoyl-CoA C27H42N7O17P3S -4 C05270 KEGG - C05270 Neutral MF = C27H46N7O18P3S SMP iasp 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 ichor Isochorismate C10H8O6 -2 C00885 KEGG - C00885 Neutral MF = C10H10O6 SMP CHS icit Isocitrate C6H5O7 -3 30810-51-6 C00311 KEGG - C00311 Neutral MF = C6H8O7 SMP CHS icolipa inner core oligosaccharide lipid A (E coli) C145H251N2O74P4 -11 AMF idon-L L-Idonate C6H11O7 -1 1114-17-6 C00770 KEGG - C00770 Neutral-C6H12O7 JLR idp IDP C10H11N4O11P2 -3 86-04-4 C00104 KEGG - C00104 Neutral MF = C10H14N4O11P2 SMP CHS Checked N-groups JLR ile-L L-Isoleucine C6H13NO2 0 73-32-5 C00407 KEGG - C00407 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR iletrna L-Isoleucyl-tRNA(Ile) C6H12NOR 1 C03127 KEGG - C03127 SMP adjusted for Genomatica's change to aa - NCD imacp 3-(Imidazol-4-yl)-2-oxopropyl phosphate C6H7N2O5P -2 C01267 KEGG - C01267 Neutral MF = C6H9N2O5P SMP CHS Checked N-groups JLR imp IMP C10H11N4O8P -2 131-99-7 C00130 KEGG - C00130 Neutral MF = C10H13N4O8P SMP CHS Checked N-groups JLR indole Indole C8H7N 0 120-72-9 C00463 KEGG - C00463 Checked N-groups JLR inost myo-Inositol C6H12O6 0 87-89-8 C00137 KEGG - C00137 Neutral Compound SMP CHS ins Inosine C10H12N4O5 0 58-63-9 C00294 KEGG - C00294 Neutral Compound SMP CHS Checked N-groups JLR ipdp Isopentenyl diphosphate C5H9O7P2 -3 C00129 KEGG - C00129 Neutral MF = C5H12O7P2 SMP isetac Isethionic acid C2H5O4S -1 107-36-8 C05123 KEGG - C05123 SAB charged following taurine's charge itp ITP C10H11N4O14P3 -4 132-06-9 C00081 KEGG - C00081 Neutral MF = C10H15N4O14P3 SMP CHS Checked N-groups JLR k potassium K 1 C00238 KEGG - C00238 kdo 3-Deoxy-D-manno-2-octulosonate C8H13O8 -1 C01187 KEGG - C01187 Neutral MF = C8H14O8 SMP CHS kdo2lipid4 KDO(2)-lipid IV(A) C84H148N2O37P2 -6 C06025 KEGG C06025 Neutral C84H154N2O37P2 JLR - NH page 1043 kdo2lipid4L KDO(2)-lipid IV(A) with laurate C96H170N2O38P2 -6 C06251 C06251 NH page 1043 Neutral-C96H176N2O38P2 JLR kdo2lipid4p KDO(2)-lipid IV(A) with palmitoleoyl C100H176N2O38P2 -6 see PMID 10092655 Neutral-C100H182N2O38P2 JLR kdo8p 3-Deoxy-D-manno-octulosonate 8-phosphate C8H12O11P -3 C04478 KEGG - C04478 Neutral MF = C8H15O11P SMP CHS kdolipid4 KDO-lipid IV(A) C76H137N2O30P2 -5 C06024 KEGG- C06024 Neutral C76H142N2O30P2 JLR- kphphhlipa kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C139H241N2O70P4 -11 AMF lac-D D-Lactate C3H5O3 -1 10326-41-7 C00256 KEGG - C00256 Neutral MF = C3H6O3 SMP CHS lac-L L-Lactate C3H5O3 -1 79-33-4 C00186 KEGG - C00186 Neutral MF = C3H6O3 SMP CHS LalaDglu L-alanine-D-glutamate C8H13N2O5 -1 AMF LalaDgluMdap L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate C15H25N4O8 -1 AMF LalaDgluMdapDala L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine C18H30N5O9 -1 AMF LalaLglu L-alanine-L-glutamate C8H13N2O5 -1 AMF dont think its the same as gluala lald-L L-Lactaldehyde C3H6O2 0 598-35-6 C00424 KEGG - C00424 Neutral Compound SMP CHS lcts Lactose C12H22O11 0 63-42-3 C00243 KEGG - C00243 Neutral Compound SMP CHS leu-L L-Leucine C6H13NO2 0 61-90-5 C00123 KEGG - C00123 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR leutrna L-Leucyl-tRNA(Leu) C6H12NOR 1 C02047 KEGG -C02047 SMP adjusted for Genomatica's change to aa - NCD lgt-S (R)-S-Lactoylglutathione C13H20N3O8S -1 59-85-8 C03451 KEGG - C03451 Neutral MF = C13H21N3O8S SMP CHS Changed according to Genomatica JLR lipa KDO(2)-lipid (A) C110H196N2O39P2 -6 598-35-6 C06026 KEGG - C06026 NH page 1043 JLR lipa_cold cold adapted KDO(2)-lipid (A) C114H202N2O39P2 -6 see PMID 10092655 Neutral C114H208N2O39P2 JLR lipidA 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 lipidAds Lipid A Disaccharide C68H127N2O20P -2 C04932 tv Kegg C04932 lipidX 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 lpp lipoprotein X 0 6244-92-4 C01834 KEGG - C01834 AMF generic lipoprotein for acyl transfering lys-L L-Lysine C6H15N2O2 1 56-87-1 C00047 KEGG - C00047 Neutral MF = C6H14N2O2 SMP CHS Changed according to Genomatica JLR lystrna L-Lysine-tRNA (Lys) C6H14N2OR 2 C01931 KEGG - C01931 SMP adjusted for Genomatica's change to aa - NCD lyx-L L-Lyxose C5H10O5 0 1949-78-6 C01508 KEGG - C01508 JLR malACP 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) malcoa Malonyl-CoA C24H33N7O19P3S -5 524-14-1 C00083 KEGG - C00083 Neutral MF = C24H38N7O19P3S SMP CHS mal-L L-Malate C4H4O5 -2 97-67-6 C00149 KEGG - C00149 Neutral MF = C4H6O5 SMP CHS malt Maltose C12H22O11 0 69-79-4 C00208 KEGG - C00208 Neutral Compound SMP CHS malt6p Maltose 6'-phosphate C12H21O14P -2 None C02995 KEGG - C02995 Neutral MF = C12H23O14P SMP CHS malthp Maltoheptaose C42H72O36 0 Not in Kegg JLR malthx Maltohexaose C36H62O31 0 34620-77-4 C01936 KEGG - C01936 JLR maltpt Maltopentaose C30H52O26 0 Not in Kegg JLR malttr Maltotriose C18H32O16 0 1109-28-0 C01835 KEGG - C01835 JLR maltttr Maltotetraose C24H42O21 0 34612-38-9 C02052 KEGG - C02052 JLR man D-Mannose C6H12O6 0 3458-28-4 C00159 KEGG - C00159 Neutral Compound SMP CHS man1p D-Mannose 1-phosphate C6H11O9P -2 C03812 KEGG - C03812 Neutral MF = C6H13O9P SMP CHS man6p D-Mannose 6-phosphate C6H11O9P -2 None C00275 KEGG - C00275 Neutral MF = C6H13O9P SMP CHS man6pglyc 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 mana D-Mannonate C6H11O7 -1 C00514 KEGG - C00514 Neutral MF = C6H12O7 SMP manglyc 2(alpha-D-Mannosyl)-D-glycerate C9H15O9 -1 C11544 KEGG C11544 melib Melibiose C12H22O11 0 585-99-9 C05402 KEGG - C05402 Neutral compound CAS # covers alpha-D-(+)-Melibiose hydrate SMP CHS mercppyr Mercaptopyruvate C3H3O3S -1 C00957 KEGG - C00957 met-D D-Methionine C5H10NO2S 0 348-67-4 C00855 KEGG - C00855 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR methf 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 met-L L-Methionine C5H11NO2S 0 63-68-3 C00073 KEGG - C00073 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR metsox-R-L L-methionine-R-sulfoxide C5H11NO3S 0 MKA KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR metsox-S-L L-Methionine-S-Sulfoxide C5H11NO3S 0 C02989 KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR Kegg C02989 mettrna L-Methionyl-tRNA (Met) C5H10NOSR 1 C02430 KEGG - C02430 SMP adjusted for Genomatica's change to aa - NCD mg2 magnesium Mg 2 C00305 KEGG - C00305 SMP mi1p-D 1D-myo-Inositol 1-phosphate C6H11O9P -2 C01177 Kegg C01177 Neutral-C6H13O9P JLR micit methylisocitrate C7H7O7 -3 20298-95-7 C04593 KEGG - C04593 Neutral-C7H10O7 JLR minohp myo-Inositol hexakisphosphate C6H6O24P6 -12 C01204 KEGG - C01204 JLR mlthf 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 mmcoa-R (R)-Methylmalonyl-CoA C25H35N7O19P3S -5 C01213 KEGG - C01213 Neutral MF = C25H40N7O19P3S SMP Checked N-groups JLR mmcoa-S (S)-Methylmalonyl-CoA C25H35N7O19P3S -5 C00683 KEGG - C00683 Neutral MF = C25H40N7O19P3S SMP CHS Checked N-groups JLR mmet S-Methyl-L-methionine C6H14NO2S 1 4289-98-9 C03172 KEGG - C03172 NCD changed to protonated form, added charge - NCD mn2 Mn2+ Mn 2 None C00034 KEGG - C00034 SMP CHS mnl D-Mannitol C6H14O6 0 69-65-8 C00392 KEGG - C00392 SMP mnl1p D-Mannitol 1-phosphate C6H13O9P -2 C00644 KEGG - C00644 Neutral MF = C6H15O9P SMP mobd Molybdate MoO4 -2 C06232 KEGG - C06232 Neutral MF = H2MoO4 SMP mql8 Menaquinol 8 C51H74O2 0 C05819 KEGG - C05819 General Formula = C16H18O2(C5H8)n; n = 7 for mql7 SMP mqn8 Menaquinone 8 C51H72O2 0 84-81-1 C00828 KEGG - C00828 General Formula = C16H16O2(C5H8)n; n = 7 for mqn8; See also mq SMP CHS mso3 methanesulfonate CH3O3S -1 0 mthgxl Methylglyoxal C3H4O2 0 78-98-8 C00546 KEGG - C00546 Neutral Compound SMP CHS murein3p3p two linked disacharide tripeptide murein units (uncrosslinked, middle of chain) C68H104N12O38 -4 AMF PMID: 9751644 has a good figure murein3px3p 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 murein3px4p two disacharide linked murein units, tripeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain) C71H107N13O38 -4 AMF PMID: 9751644 has a good figure murein4p3p two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain) C71H109N13O39 -4 AMF PMID: 9751644 has a good figure murein4p4p two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain) C74H114N14O40 -4 AMF PMID: 9751644 has a good figure murein4px4p two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain) C74H112N14O39 -4 AMF PMID: 9751644 has a good figure murein4px4p4p 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 murein4px4px4p 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 murein5p3p two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain) C74H114N14O40 -4 AMF PMID: 9751644 has a good figure murein5p4p two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain) C77H119N15O41 -4 AMF PMID: 9751644 has a good figure murein5p5p 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 murein5p5p5p three linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) C120H186N24O63 -6 AMF murein5px3p 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 murein5px4p 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 murein5px4px4p 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 myrsACP 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) N1aspmd N1-Acetylspermidine C9H23N3O 2 34450-16-3 C00612 KEGG - C00612 JLR capitalized N at beginning of abbrev -NCD Checked N-groups JLR n2o Nitrous oxide N2O 0 10024-97-2 C00887 KEGG - C00887 SMP CHS n8aspmd N8-Acetylspermidine C9H23N3O 2 34450-15-2 C01029 KEGG - C01029 JLR Checked N-groups JLR na1 Sodium Na 1 7440-23-5 C01330 KEGG - C01330 SMP CHS nac Nicotinate C6H4NO2 -1 59-67-6 C00253 KEGG - C00253 Neutral MF = C6H5NO2 SMP CHS Checked N-groups JLR nad 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) nadh 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 nadp Nicotinamide adenine dinucleotide phosphate C21H25N7O17P3 -3 53-59-8 C00006 KEGG - C00006 Original KEGG MF = C21H29N7O17P3 (+1) SMP CHS Checked N-groups JLR nadph 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 ncam Nicotinamide C6H6N2O 0 98-92-0 C00153 KEGG - C00153 SMP CHS Checked N-groups JLR nh4 Ammonium H4N 1 66701-25-5 C01342 KEGG - C01342 Charged Compound Diiferentiate Ammonia from Ammonium SMP CHS Checked N-groups JLR ni2 nickel Ni 2 C00291 KEGG - C00291 nicrnt Nicotinate D-ribonucleotide C11H12NO9P -2 C01185 KEGG - C01185 Neutral MF = C11H15NO9P SMP Checked N-groups JLR nmn NMN C11H14N2O8P -1 1094-61-7 C00455 KEGG - C00455 Correct MF = C11H16N2O8P KEGG MF = C11H15N2O8P with charge +1 SMP Checked N-groups JLR Nmtrp N-Methyltryptophan C12H14N2O2 0 526-31-8 C02983 KEGG - C02983 no Nitric oxide NO 0 10102-43-9 C00533 KEGG - C00533 SMP CHS no2 Nitrite NO2 -1 7697-37-2 C00088 KEGG - C00088 Neutral MF = HNO2 SMP CHS Checked N-groups JLR no3 Nitrate NO3 -1 C00244 KEGG - C00244 Neutral MF = HNO3 SMP CHS Checked N-goups JLR o16a2und (O16 antigen)x2 undecaprenyl diphosphate C123H200N2O57P2 -2 AMF o16a3und (O16 antigen)x3 undecaprenyl diphosphate C157H255N3O82P2 -2 AMF o16a4colipa (O16 antigen)x4 core oligosaccharide lipid A C312H523N6O200P4 -11 AMF o16a4und (O16 antigen)x4 undecaprenyl diphosphate C191H310N4O107P2 -2 AMF o16aund O16 antigen undecaprenyl diphosphate C89H145N1O32P2 -2 AMF - structure from PMID: 7517391 o2 O2 O2 0 7782-44-7 C00007 KEGG - C00007 SMP CHS o2- Superoxide anion O2 -1 C00704 KEGG - C00704 JLR oaa Oxaloacetate C4H2O5 -2 328-42-7 C00036 KEGG - C00036 Neutral MF = C4H4O5 SMP CHS oc2coa trans-Oct-2-enoyl-CoA C29H44N7O17P3S -4 C05276 KEGG - C05276 Neutral MF = C29H48N7O18P3S SMP ocACP Octanoyl-ACP (n-C8:0ACP) C19H35N2O8PRS -1 JLR- saturated fatty acid with 8 carbons attached to ACP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) occoa Octanoyl-CoA (n-C8:0CoA) C29H46N7O17P3S -4 C01944 KEGG - C01944 Neutral MF = C29H50N7O17P3S SMP ocdca 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 ocdcea octadecenoate (n-C18:1) C18H33O2 -1 monounsaturated fatty acid, 18 carbons KEGG - C00712 NCD updated by NJ octa octanoate (n-C8:0) C8H15O2 -1 124-07-2 C06423 KEGG - C06423 Neutral MF = C8H16O2 SMP changed compound class from peptides - NCD octdp all-trans-Octaprenyl diphosphate C40H65O7P2 -3 C04146 KEGG - C04146 Neutral MF = C40H68O7P2 SMP octeACP Octadecenoyl-ACP (n-C18:1ACP) C29H53N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) od2coa trans-Octadec-2-enoyl-CoA C39H64N7O17P3S -4 NCD C18:1 - C18H33O2 (charge -1) C21H32N7O16P3S (charge -4) NJ odecoa Octadecenoyl-CoA (n-C18:1CoA) C39H64N7O17P3S -4 NCD KEGG - C00510 C18:1 C18H33O2 (charge -1) CoA - C21H32N7O16P3S charge (-4) NJ ohpb 2-Oxo-3-hydroxy-4-phosphobutanoate C4H4O8P -3 C06054 KEGG - C06054 Neutral-C4H7O8P JLR op4en 2-Oxopent-4-enoate C5H5O3 -1 C00596 KEGG - C00596 Neutral-C5H6O3 JLR orn Ornithine C5H13N2O2 1 70-26-8 C01602 KEGG - C01602 Neutral MF = C5H12N2O2 SMP CHS Checked N-groups JLR orot Orotate C5H3N2O4 -1 65-86-1 C00295 KEGG - C00295 Neutral MF = C5H4N2O4 SMP CHS Checked N-groups JLR orot5p Orotidine 5'-phosphate C10H10N2O11P -3 2149-82-8 C01103 KEGG - C01103 Neutral MF = C10H13N2O11P SMP Checked N-groups JLR oxam Oxamate C2H2NO3 -1 471-47-6 C01444 KEGG - C01444 JLR- Checked protonation state oxur Oxalureate C3H3N2O4 -1 585-05-7 C00802 KEGG - C00802 Checked Protonation state JLR pa_EC phosphatidate (E.coli) C1836H3398O400P50 -100 C00416 tv org: Hpylori, Ecoli phosphatidate (50x scaled up) with 2 ave fatty acids JLR- needs to be -100 charge pac Phenylacetic acid C8H7O2 -1 CAS: 103-82-2 C07086 Kegg C07086 Neutral-C8H8O2 JLR pacald Phenylacetaldehyde C8H8O 0 122-78-1 C00601 KEGG - C00601 JLR palmACP Palmitoyl-ACP (n-C16:0ACP) C27H51N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) pan4p Pantetheine 4'-phosphate C11H21N2O7PS -2 C01134 KEGG - C01134 Neutral MF = C11H23N2O7PS SMP CHS Checked N-groups JLR pant-R (R)-Pantoate C6H11O4 -1 470-29-1 C00522 KEGG - C00522 Neutral MF = C6H12O4 SMP CHS pap Adenosine 3',5'-bisphosphate C10H11N5O10P2 -4 1053-73-2 C00054 KEGG - C00054 Neutral MF = C10H15N5O10P2 SMP CHS paps 3'-Phosphoadenylyl sulfate C10H11N5O13P2S -4 482-67-7 C00053 KEGG - C00053 Neutral MF = C10H15N5O13P2S SMP Checked N-groups JLR pc_EC Phosphatidylcholine (E.coli) C2086H4048N50O400P50 0 C00157 Scaled up by 50, really is 50 molecules or phosphatidylcholine. Scale was used so that the elements were whole numbers. JLR pdx5p Pyridoxine 5'-phosphate C8H10NO6P -2 447-05-2 C00627 KEGG - C00627 Neutral MF = C8H12NO6P SMP CHS Checked N-groups JLR pe_EC Phosphatidylethanolamine (ecoli) C1936H3748N50O400P50 0 C00350 tv org: Hpylori, Ecoli scaled up (50x) of ps with 2 ave fatty acids Checked N JLR peamn Phenethylamine C8H12N 1 64-04-0 C05332 KEGG - C05332 JLR Checked N-groups JLR pep Phosphoenolpyruvate C3H2O6P -3 138-08-9 C00074 KEGG - C00074 Neutral MF = C3H5O6P SMP CHS pg_EC Phosphatidylglycerol (Ecoli) C1986H3748O500P50 -50 C00344 tv org: Ecoli scaled up (50x) of phosphatidylglycerol with an ave fatty acid of C1686 H3148 O100 pgp_EC Phosphatidylglycerophosphate (Ecoli) C1986H3698O650P100 -150 C03892 tv org: Ecoli scaled up (50x) of phosphatidylglycerophosphate with 2 ave fatty acid chain (C1686 H3148 O100) phaccoa Phenylacetyl-CoA C29H38N7O17P3S -4 C00582 KEGG - C00582 Neutral-C29H42N7O17P3S JLR phe-L L-Phenylalanine C9H11NO2 0 63-91-2 C00079 KEGG - C00079 Neutral MF = C9H11NO2 SMP CHS Changed according to Genomatica JLR pheme 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 phetrna L-Phenylalanyl-tRNA(Phe) C9H10NOR 1 C03511 KEGG - C03511 SMP adjusted for Genomatica's change to aa - NCD phhlipa phospho-heptosyl-heptosyl-kdo2-lipidA C124H219N2O54P3 -8 AMF phom O-Phospho-L-homoserine C4H8NO6P -2 C01102 KEGG - C01102 Neutral MF = C4H10NO6P SMP CHS Changed according to Genomatica JLR phphhlipa phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H230N2O63P4 -10 AMF phpyr Phenylpyruvate C9H7O3 -1 156-06-9 C00166 KEGG - C00166 Neutral MF = C9H8O3 SMP CHS phthr O-Phospho-4-hydroxy-L-threonine C4H8NO7P -2 C06055 KEGG - C06055 NCD Checked N-groups JLR pi Phosphate HO4P -2 14265-44-2 C00009 KEGG - C00009 Neutral MF = H3O4P SMP CHS Formula changed to HPO4 (Charge -2) on Feb-26-2002 pmcoa Pimeloyl-CoA C28H41N7O19P3S -5 C01063 KEGG - C01063 Neutral MF = C28H46N7O19P3S SMP CHS pmtcoa 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 pnto-R (R)-Pantothenate C9H16NO5 -1 79-83-4 C00864 Deleted KEGG - C00864 KEGG - C02349 Neutral MF = C9H17NO5 SMP CHS Checked N-groups JLR ppa Propionate (n-C3:0) C3H5O2 -1 79-09-4 C00163 KEGG - C00163 Neutral MF = C3H6O2 SMP NCD ppal Propanal C3H6O 0 123-38-6 C00479 KEGG - C00479 Neutral Compound SMP ppap Propanoyl phosphate C3H5O5P -2 121-69-7 C02876 KEGG - C02876 Neutral: C3H7O5P JLR ppbng Porphobilinogen C10H13N2O4 -1 487-90-1 C00931 KEGG - C00931 Neutral MF = C10H14N2O4 SMP Changed according to Genomatica JLR ppcoa Propanoyl-CoA C24H36N7O17P3S -4 317-66-8 C00100 KEGG - C00100 Neutral MF = C24H40N7O17P3S SMP CHS NCD ppgpp Guanosine 3',5'-bis(diphosphate) C10H11N5O17P4 -6 C01228 KEGG - C01228 Neutral MF = C10H17N5O17P4 SMP pphn Prephenate C10H8O6 -2 126-49-8 C00254 KEGG - C00254 Neutral MF = C10H10O6 SMP CHS ppi Diphosphate HO7P2 -3 09/03/2466 C00013 KEGG - C00013 Neutral MF = H4O7P2 SMP CHS Formula changed to HO7P2 (Charge -3) on Feb-26-2002 ppp9 Protoporphyrin C34H32N4O4 -2 553-12-8 C02191 KEGG - C02191 Neutral MF = C34H34N4O4 SMP CHS pppg9 Protoporphyrinogen IX C34H38N4O4 -2 C01079 KEGG - C01079 Neutral MF = C34H40N4O4 SMP Checked N-groups JLR pppi Inorganic triphosphate HO10P3 -4 C03279 KEGG - C03279 Neutral MF = H5O10P3 SMP pppn Phenylpropanoate C9H9O2 -1 2628-17-3 C05629 KEGG - C05629 Neutral-C9H10O2 JLR ppt Phosphonate HO3P -2 13598-36-2 C06701 KEGG - C06701 JLR Pka- 2 and 6.58 (http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf) pram 5-Phospho-beta-D-ribosylamine C5H11NO7P -1 C03090 KEGG - C03090 Neutral MF = C5H12NO7P SMP CHS Changed according to Genomatica JLR pran N-(5-Phospho-D-ribosyl)anthranilate C12H13NO9P -3 None C04302 KEGG - C04302 Neutral MF = C12H16NO9P SMP CHS Checked N-groups JLR prbamp 1-(5-Phosphoribosyl)-AMP C15H19N5O14P2 -4 C02741 KEGG - C02741 Neutral MF = C15H23N5O14P2 SMP CHS prbatp 1-(5-Phosphoribosyl)-ATP C15H19N5O20P4 -6 C02739 KEGG - C02739 Neutral MF = C15H25N5O20P4 SMP CHS prfp 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 prlp 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 pro-L L-Proline C5H9NO2 0 147-85-3 C00148 KEGG - C00148 Neutral MF = C5H9NO2 SMP CHS Changed according to Genomatica JLR protrna L-Prolyl-tRNA(Pro) C5H8NOR 1 C02702 KEGG - C02702 SMP adjusted for Genomatica's change to aa - NCD prpp 5-Phospho-alpha-D-ribose 1-diphosphate C5H8O14P3 -5 C00119 KEGG - C00119 Neutral MF = C5H13O14P3 SMP ps_EC phosphatidylserine (Ecoli) C1986H3698N50O500P50 -50 C02737 tv org: Hpylori, Ecoli scaled up (50x) of phosphatidylserine with an average 2 fatty acid chain (C1686H3148O100) Checked N JLR pser-L O-Phospho-L-serine C3H6NO6P -2 407-41-0 C01005 KEGG - C01005 Neutral MF = C3H8NO6P SMP Changed according to Genomatica JLR ptrc Putrescine C4H14N2 2 110-60-1 C00134 KEGG - C00134 Neutral Compound SMP CHS Changed according to Genomatica JLR pyam5p Pyridoxamine 5'-phosphate C8H12N2O5P -1 529-96-4 C00647 KEGG - C00647 Neutral MF = C8H13N2O5P SMP CHS Checked N-groups JLR, AMF pydam Pyridoxamine C8H13N2O2 1 85-87-0 C00534 KEGG - C00534 Neutral Compound SMP CHS Checked N-groups JLR, AMF pydx Pyridoxal C8H9NO3 0 66-72-8 C00250 KEGG - C00250 Neutral Compound SMP CHS Checked N-groups JLR pydx5p Pyridoxal 5'-phosphate C8H8NO6P -2 54-47-7 C00018 KEGG - C00018 Neutral MF = C8H10NO6P SMP CHS Checked N-groups JLR, AMF pydxn Pyridoxine C8H11NO3 0 65-23-6 C00314 KEGG - C00314 Neutral Compound SMP CHS Checked N-groups JLR pyr Pyruvate C3H3O3 -1 127-17-3 C00022 KEGG - C00022 Neutral MF = C3H4O3 SMP CHS q8 Ubiquinone-8 C49H74O4 0 1339-63-5 C00399 KEGG C00399 Formula- C14H18O4(C5H8)n , where n=7 for q8 JLR q8h2 Ubiquinol-8 C49H76O4 0 C00390 KEGG C00390 JLR quln Quinolinate C7H3NO4 -2 89-00-9 C03722 KEGG - C03722 Neutral MF = C7H5NO4 SMP CHS Checked N-groups JLR r15bp D-Ribose 1,5-bisphosphate C5H8O11P2 -4 None C01151 KEGG - C01151 Neutral MF = C5H12O11P2 SMP CHS r1p alpha-D-Ribose 1-phosphate C5H9O8P -2 58459-37-3 C00442 KEGG - C00442 Neutral MF = C5H11O8P SMP CHS r5p alpha-D-Ribose 5-phosphate C5H9O8P -2 4300-28-1 C00117 KEGG - C00117 Delete KEGG - C03736 Neutral MF = C5H11O8P SMP CHS ragund rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C69H113N1O16P2 -2 AMF rbflvrd Reduced riboflavin C17H22N4O6 0 C01007 KEGG - C01007 rbl-L L-Ribulose C5H10O5 0 488-84-6 C00508 KEGG - C00508 Neutral Compound SMP CHS rbt Ribitol C5H12O5 0 488-81-3 C00474 KEGG - C00474 SMP rbt5p D-Ribitol 5-phosphate C5H11O8P -2 C01068 KEGG - C01068 Neutral MF = C5H13O8P SMP rdmbzi N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole C14H18N2O4 0 C05775 KEGG - C05775 SMP JLR Checked N-groups JLR rhcys S-Ribosyl-L-homocysteine C9H17NO6S 0 37558-16-0 C03539 KEGG - C03539 Neutral-C9H17NO6S JLR Checked N-groups JLR rib-D D-Ribose C5H10O5 0 50-69-1 C00121 KEGG - C00121 Neutral Compound SMP CHS ribflv Riboflavin C17H20N4O6 0 83-88-5 C00255 KEGG - C00255 Neutral Compound SMP CHS rml L-Rhamnulose C6H12O5 0 C00861 KEGG - C00861 SMP rml1p L-Rhamnulose 1-phosphate C6H11O8P -2 C01131 KEGG - C01131 Neutral MF = C6H13O8P SMP rmn L-Rhamnose C6H12O5 0 3615-41-6 C00507 KEGG - C00507 SMP ru5p-D D-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C00199 KEGG - C00199 Neutral MF = C5H11O8P Error in Chemfinder molecular formula SMP CHS ru5p-L L-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C01101 KEGG - C01101 Neutral MF = C5H11O8P SMP s7p Sedoheptulose 7-phosphate C7H13O10P -2 None C00281 KEGG - C00281 Neutral MF = C7H15O10P SMP CHS sarcs Sarcosine C3H7NO2 0 107-97-1 C00213 KEGG - C00213 SAB sbt6p D-Sorbitol 6-phosphate C6H13O9P -2 108392-12-7 C01096 KEGG - C01096 Neutral MF = C6H15O9P SMP CHS sbt-D D-Sorbitol C6H14O6 0 50-70-4 C00794 KEGG - C00794 Neutral Compound SMP CHS sbzcoa O-Succinylbenzoyl-CoA C32H39N7O20P3S -5 C03160 KEGG - C03160 Neutral MF = C32H44N7O20P3S SMP CHS scl sirohydrochlorin C42H39N4O16 -7 C05778 KEGG - C05778 Neutral MF = C42H46N4O16 SMP Checked N-groups, JLR scsertrna L-Selenocysteinyl-tRNA(Ser) C3H6NO2R 1 16561-29-8 C05173 KEGG - C05173 seln Selenide HSe -1 531-44-2 C01528 KEGG - C01528 Neutral-H2Se JLR selnp Selenophosphate H2O3PSe -1 16561-29-8 C05172 KEGG - C05172 Neutral H3O3PSe JLR seramp L-seryl-AMP C13H19N6O9P 0 See EcoCyc- L-seryl-AMP JLR Checked N-groups JLR ser-D D-Serine C3H7NO3 0 312-84-5 C00740 KEGG - C00740 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR ser-L L-Serine C3H7NO3 0 56-45-1 C00065 KEGG - C00065 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR sertrna L-Seryl-tRNA(Ser) C3H6NO2R 1 C02553 KEGG - C02553 SMP adjusted for Genomatica's change to aa - NCD Sfglutth S-Formylglutathione C11H16N3O7S -1 C01031 KEGG - C01031 NCD changed to protonated form, added +1 charge - NCD sheme 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 skm Shikimate C7H9O5 -1 138-59-0 C00493 KEGG - C00493 Neutral MF = C7H10O5 SMP CHS skm5p Shikimate 5-phosphate C7H8O8P -3 C03175 KEGG - C03175 Neutral MF = C7H11O8P SMP CHS sl26da N-Succinyl-LL-2,6-diaminoheptanedioate C11H16N2O7 -2 C04421 KEGG - C04421 Neutral MF = C11H18N2O7 SMP CHS Changed according to Genomatica JLR sl2a6o N-Succinyl-2-L-amino-6-oxoheptanedioate C11H12NO8 -3 C04462 KEGG - C04462 Neutral MF = C11H15NO8 SMP CHS Checked N-groups JLR so2 sulfur dioxide O2S 0 C09306 AMF so3 Sulfite O3S -2 7782-99-2 C00094 KEGG - C00094 Neutral MF = H2O3S (sulfurous acid) SMP CHS so4 Sulfate O4S -2 7664-93-9 C00059 KEGG - C00059 Neutral MF = H2O4S (sulfuric acid) SMP CHS spmd Spermidine C7H22N3 3 124-20-9 C00315 KEGG - C00315 Neutral Compound SMP CHS Changed according to Genomatica JLR ssaltpp Succinate semialdehyde-thiamin diphosphate anion C16H21N4O10P2S -3 C05816 KEGG - C05816 Neutral MF = C16H24N4O10P2S SMP JLR Checked N-groups JLR stcoa Stearoyl-CoA (n-C18:0CoA) C39H66N7O17P3S -4 362-66-3 C00412 KEGG - C00412 NCD SMP (2/7/03) C18:0 + CoA suc6p Sucrose 6-phosphate C12H21O14P -2 C02591 KEGG - C02591 Neutral MF = C12H23O14P SMP CHS sucarg N2-Succinyl-L-arginine C10H17N4O5 -1 1758-80-1 C03296 KEGG - C03296 Neutral:C10H18N4O5 JLR Checked N-groups JLR sucbz o-Succinylbenzoate C11H8O5 -2 C02730 KEGG - C02730 Neutral MF = C11H10O5 SMP CHS succ Succinate C4H4O4 -2 110-15-6 C00042 KEGG - C00042 Neutral MF = C4H6O4 SMP CHS succoa Succinyl-CoA C25H35N7O19P3S -5 604-98-8 C00091 KEGG - C00091 Neutral MF = C25H40N7O19P3S SMP CHS checked N groups - NCD sucglu N2-Succinyl-L-glutamate C9H10NO7 -3 2009-64-5 C05931 KEGG - C05931 Neutral: C9H13NO7 JLR Checked N-groups JLR sucgsa N2-Succinyl-L-glutamate 5-semialdehyde C9H11NO6 -2 2009-64-5 C05932 KEGG - C05932 Neutral: C9H13NO6 JLR Checked N-groups JLR suchms O-Succinyl-L-homoserine C8H12NO6 -1 1492-23-5 C01118 KEGG - C01118 Neutral MF = C8H13NO6 SMP CHS Changed according to Genomatica JLR sucorn N2-Succinyl-L-ornithine C9H15N2O5 -1 80102-04-1 C03415 KEGG - C03415 Neutral: C9H16N2O5 JLR Checked N-groups JLR sucr Sucrose C12H22O11 0 57-50-1 C00089 KEGG - C00089 sucsal Succinic semialdehyde C4H5O3 -1 692-29-5 C00232 KEGG - C00232 Neutral MF = C4H6O3 SMP CHS sulfac sulfoacetate C2H2O5S -2 AMF tag6p-D D-Tagatose 6-phosphate C6H11O9P -2 C01097 KEGG - C01097 Neutral MF=C6H13O9P JLR tagdp-D D-Tagatose 1,6-biphosphate C6H10O12P2 -4 C03785 KEGG - C03785 Neutral MF = C6H14O12P2 NCD tagur D-Tagaturonate C6H9O7 -1 None C00558 KEGG - C00558 Neutral MF = C6H10O7 SMP CHS tartr-L L-tartrate C4H4O6 -2 87-69-4 C00898 KEGG - C00898 Neutral-C4H6O6 JLR taur Taurine C2H7NO3S 0 107-35-7 C00245 KEGG - C00245 Neutral MF = C2H7NO3S SMP Changed according to Genomatica JLR tcynt Thiocyanate CNS -1 463-56-9 C01755 KEGG - C01755 Neutral-CHNS JLR Checked N-groups JLR td2coa trans-Tetradec-2-enoyl-CoA C35H56N7O17P3S -4 C05273 KEGG - C05273 Neutral MF = C35H60N7O17P3S SMP tdcoa Tetradecanoyl-CoA (n-C14:0CoA) C35H58N7O17P3S -4 C02593 KEGG - C02593 Neutral MF = C35H62N7O17P3S SMP changed compound class from peptides to fatty acids - NCD tdeACP Tetradecenoyl-ACP (n-C14:1ACP) C25H45N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) thdp 2,3,4,5-Tetrahydrodipicolinate C7H7NO4 -2 52-52-8 C03972 KEGG - C03972 Neutral MF = C7H9NO4 SMP CHS Checked N-groups JLR thf 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 thm 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 thmmp Thiamin monophosphate C12H16N4O4PS -1 532-40-1 C01081 KEGG - C01081 +1 Charged MF = C12H18N4O4PS SMP CHS Checked N-groups JLR thmpp 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 thr-D D-Threonine C4H9NO3 0 632-20-2 C00820 KEGG - C00820 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR thr-L L-Threonine C4H9NO3 0 72-19-5 C00188 KEGG - C00188 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR thrp L-Threonine O-3-phosphate C4H8NO6P -2 C12147 AMF C12147 thrtrna L-Threonyl-tRNA(Thr) C4H8NO2R 1 C02992 KEGG - C02992 SMP adjusted for Genomatica's change to aa - NCD thym Thymine C5H6N2O2 0 65-71-4 C00178 KEGG - C00178 Neutral Compound SMP CHS thymd Thymidine C10H14N2O5 0 50-89-5 C00214 KEGG - C00214 Neutral Compound SMP CHS Checked N-groups JLR tma trimethylamine C3H10N 1 75-50-3 C00565 KEGG - C00565 pKa=9.8 Checked N-groups JLR tmao Trimethylamine N-oxide C3H9NO 0 1184-78-7 C01104 KEGG - C01104 Zwitter ion, pKa =4.65 Checked N-groups JLR trdox Oxidized thioredoxin X 0 C00343 KEGG - C00343 SMP trdrd Reduced thioredoxin XH2 0 C00342 KEGG - C00342 SMP tre Trehalose C12H22O11 0 99-20-7 C01083 KEGG - C01083 Neutral Compound SMP tre6p alpha,alpha'-Trehalose 6-phosphate C12H21O14P -2 4484-88-2 C00689 KEGG - C00689 Neutral MF = C12H23O14P SMP CHS trnaala tRNA(Ala) R 0 C01635 KEGG - C01635 SMP trnaarg tRNA(Arg) R 0 C01636 KEGG - C01636 SMP trnaasn tRNA(Asn) R 0 C01637 KEGG - C01637 SMP trnaasp tRNA(Asp) R 0 C01638 KEGG - C01638 SMP trnacys tRNA(Cys) R 0 C01639 KEGG - C01639 SMP trnagln tRNA(Gln) R 0 C01640 KEGG - C01640 SMP trnaglu tRNA (Glu) R 0 None C01641 KEGG - C01641 X = (C5H8O6PR)n Represent as uncharged species SMP; MF changed on May 7, 2002 CHS trnagly tRNA(Gly) R 0 C01642 KEGG - C01642 SMP trnahis tRNA(His) R 0 C01643 KEGG - C01643 SMP trnaile tRNA(Ile) R 0 C01644 KEGG - C01644 SMP trnaleu tRNA(Leu) R 0 C01645 KEGG - C01645 SMP trnalys tRNA(Lys) R 0 C01646 KEGG - C01646 SMP trnamet tRNA(Met) R 0 C01647 KEGG - C01647 SMP trnaphe tRNA(Phe) R 0 C01648 KEGG - C01648 SMP trnapro tRNA(Pro) R 0 C01649 KEGG - C01649 SMP trnasecys tRNA(SeCys) R 0 0 trnaser tRNA(Ser) R 0 C01650 KEGG - C01650 SMP trnathr tRNA(Thr) R 0 C01651 KEGG - C01651 SMP trnatrp tRNA(Trp) R 0 C01652 KEGG - C01652 SMP trnatyr tRNA(Tyr) R 0 C00787 KEGG - C00787 SMP trnaval tRNA(Val) R 0 C01653 KEGG - C01653 SMP trp-L L-Tryptophan C11H12N2O2 0 73-22-3 C00078 KEGG - C00078 Neutral MF = C11H12N2O2 SMP CHS Changed according to Genomatica JLR trptrna L-Tryptophanyl-tRNA(Trp) C11H11N2OR 1 C03512 KEGG - C03512 SMP adjusted for Genomatica's change to aa - NCD tsul Thiosulfate O3S2 -2 C00320 KEGG - C00320 Neutral MF = H2O3S2 SMP ttdca 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 ttdcea tetradecenoate (n-C14:1) C14H25O2 -1 monounsaturated fatty acid, 14 carbons NCD tungs tungstate O4W1 -2 AMF tym Tyramine C8H12NO 1 51-67-2 C00483 KEGG - C00483 AMF tyr-L L-Tyrosine C9H11NO3 0 60-18-4 C00082 KEGG - C00082 Neutral MF = C9H11NO3 SMP CHS Changed according to Genomatica JLR tyrp Phosphotyrosine C9H10NO6P -2 7625-23-2 C06501 KEGG - C06501 tyrtrna L-Tyrosyl-tRNA(Tyr) C9H10NO2R 1 C02839 KEGG - C02839 SMP adjusted for Genomatica's change to aa - NCD u23ga UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine C43H75N3O20P2 -2 C04652 KEGG - C04652 Neutral MF = C43H77N3O20P2 SMP CHS Checked N-groups JLR u3aga UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine C31H51N3O19P2 -2 C04738 KEGG - C04738 Neutral MF = C31H53N3O19P2 SMP CHS Checked N-groups JLR u3hga UDP-3-O-(3-hydroxytetradecanoyl)-D-glucosamine C29H50N3O18P2 -1 C06022 KEGG - C06022 Neutral MF = C29H51N3O18P2 SMP CHS Checked N-groups JLR uaagmda 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 uaccg UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine C20H26N3O19P2 -3 C04631 KEGG - C04631 Neutral MF = C20H29N3O19P2 SMP CHS Checked N-groups JLR uacgam UDP-N-acetyl-D-glucosamine C17H25N3O17P2 -2 C00043 KEGG - C00043 KEGG glycan: G10610 Neutral MF = C17H27N3O17P2 SMP CHS Checked N-groups JLR uacmam 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 uacmamu UDP-N-acetyl-D-mannosaminouronate C17H22N3O18P2 -3 90-02-8 C06240 KEGG - C06240 Neutral-C17H25N3O18P2 JLR Checked N-groups JLR uagmda 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 uama UDP-N-acetylmuramoyl-L-alanine C23H33N4O20P2 -3 C01212 KEGG - C01212 Neutral MF = C23H36N4O20P2 SMP CHS Checked N-groups JLR uamag UDP-N-acetylmuramoyl-L-alanyl-D-glutamate C28H39N5O23P2 -4 C00692 KEGG - C00692 Neutral MF = C28H43N5O23P2 SMP CHS Checked N-groups JLR uamr UDP-N-acetylmuramate C20H28N3O19P2 -3 C01050 KEGG - C01050 Neutral MF = C20H31N3O19P2 SMP CHS Checked N-groups JLR udcpdp Undecaprenyl diphosphate C55H89O7P2 -3 C03543 KEGG - C03543 Neutral MF = C55H92O7P2 SMP CHS udcpp Undecaprenyl phosphate C55H89O4P -2 C00348 KEGG - C00348 Neutral MF = C55H91O4P SMP CHS udp UDP C9H11N2O12P2 -3 58-98-0 C00015 KEGG - C00015 Neutral MF = C9H14N2O12P2 SMP CHS udpacgal UDP-N-acetyl-D-galactosamine C17H25N3O17P2 -2 None C00203 KEGG - C00203 changed to proper charge - NCD udpg UDPglucose C15H22N2O17P2 -2 C00029 KEGG - C00029 Neutral MF = C15H24N2O17P2 SMP CHS udpgal UDPgalactose C15H22N2O17P2 -2 C00052 KEGG - C00052 Neutral MF = C15H24N2O17P2 SMP CHS udpgalfur UDP-D-galacto-1,4-furanose C15H22N2O17P2 -2 638-23-3 C03733 KEGG - C03733 Neutral-C15H24N2O17P2 JLR Checked N-groups JLR udpglcur UDP-D-glucuronate C15H19N2O18P2 -3 C00167 KEGG - C00167 Neutral-C15H22N2O18P2 JLR Checked N-groups JLR udpLa4fn uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose C15H21N3O16P2 -2 AMF udpLa4n uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose C14H22N3O15P2 -1 AMF udpLa4o UDP-4-keto-pyranose C14H18N2O16P2 -2 AMF ugmd 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 ugmda 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 uLa4fn undecaprenyl phosphate-4-amino-4-formyl-L-arabinose C61H99N1O8P1 -1 AMF uLa4n undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose C60H100N1O7P1 0 AMF um4p UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine C38H56N8O27P2 -4 AMF ump UMP C9H11N2O9P -2 58-97-9 C00105 KEGG - C00105 Neutral MF = C9H13N2O9P SMP CHS unaga Undecaprenyl diphospho N-acetyl-glucosamine C63H103NO12P2 -2 Not in Kegg Neutral-C63H105NO12P2 JLR Checked N-groups unagamu Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate C71H113N2O18P2 -3 No Kegg entry Neutral-C71H116N2O18P2 JLR Checked N-groups JLR unagamuf 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 uppg3 Uroporphyrinogen III C40H36N4O16 -8 1976-85-8 C01051 KEGG - C01051 Neutral MF = C40H44N4O16 SMP CHS Checked N-groups JLR ura Uracil C4H4N2O2 0 66-22-8 C00106 KEGG - C00106 Neutral Compound SMP CHS urate Urate C5H4N4O3 0 69-93-2 C00366 KEGG - C00366 Neutral Compound SMP CHS urdglyc (-)-Ureidoglycolate C3H5N2O4 -1 C00603 KEGG - C00603 Neutral- C4H6N2O4 JLR Checked N-groups JLR urea Urea CH4N2O 0 57-13-6 C00086 KEGG - C00086 Neutral Compound SMP CHS Checked N-groups JLR uri Uridine C9H12N2O6 0 58-96-8 C00299 KEGG - C00299 Neutral Compound SMP CHS Checked N-groups JLR utp UTP C9H11N2O15P3 -4 63-39-8 C00075 KEGG - C00075 Neutral MF = C9H15N2O15P3 SMP CHS val-L L-Valine C5H11NO2 0 72-18-4 C00183 KEGG - C00183 Neutral MF = C5H11NO2 SMP CHS Changed according to Genomatica JLR valtrna L-Valyl-tRNA(Val) C5H10NOR 1 C02554 KEGG - C02554 SMP adjusted for Genomatica's change to aa - NCD xan Xanthine C5H4N4O2 0 69-89-6 C00385 KEGG - C00385 Neutral Compound SMP CHS Checked N-groups JLR xmp Xanthosine 5'-phosphate C10H11N4O9P -2 523-98-8 C00655 KEGG - C00655 Neutral MF = C10H13N4O9P SMP CHS Checked N-groups JLR xtp XTP C10H11N4O15P3 -4 C00700 KEGG - C00700 IT xtsn Xanthosine C10H12N4O6 0 146-80-5 C01762 KEGG - C01762 Neutral Compound SMP CHS Checked N-groups JLR xu5p-D D-Xylulose 5-phosphate C5H9O8P -2 None C00231 KEGG - C00231 Neutral MF = C5H11O8P SMP CHS xu5p-L 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 xyl-D D-Xylose C5H10O5 0 58-86-6 C00181 KEGG - C00181 Neutral Compound SMP CHS xylu-D D-Xylulose C5H10O5 0 551-84-8 C00310 KEGG - C00310 Neutral Compound SMP CHS xylu-L L-Xylulose C5H10O5 0 527-50-4 C00312 KEGG - C00312 Neutral Compound SMP CHS zn2 Zinc Zn 2 7440-66-6 C00038 KEGG - C00038 Biomass Biomass