{"ymdb_id":"YMDB00535","created_at":"2011-05-29T18:28:09.000Z","updated_at":"2016-09-08T18:35:35.000Z","name":"(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid","cas":"20298-95-7","state":"Solid","melting_point":null,"description":"(2S,3R)-3-Hydroxybutane-1,2,3-tricarboxylic acid is a product of bacterial metabolism in the gut. It can be produced by 2-methylisocitrate lyase and by 2-methylisocitrate dehydratase.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"-7.999","location":null,"synthesis_reference":null,"chebi_id":"15607","hmdb_id":"HMDB03529","kegg_id":"C04593","pubchem_id":"5459784","cs_id":"4573561","foodb_id":null,"wikipedia_link":null,"biocyc_id":null,"iupac":"(1R,2S)-1-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid","traditional_iupac":"methylisocitrate","logp":"-1.0135623636666664","pka":"4.805179537739236","alogps_solubility":"1.49e+02 g/l","alogps_logp":"-0.87","alogps_logs":"-0.14","acceptor_count":"7","donor_count":"4","rotatable_bond_count":"5","polar_surface_area":"132.13","refractivity":"40.4294","polarizability":"17.258105682756803","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"-4.066922204255973","pka_strongest_acidic":"3.1668703375685876","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2s,3r)-3-hydroxybutane-1,2,3-tricarboxylate","(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylic acid","1D-myo-Inositol 1,3,4,5,6-pentakisphosphate","D-myo-Inositol 1,3,4,5,6-pentakisphosphate","Inositol 1,3,4,5,6-pentakisphosphate","Inositol 1,3,4,5,6-pentaphosphate","Inositol pentaphosphate","methylisocitrate","methylisocitric acid","myo-Inositol 1,3,4,5,6-pentakis(phosphate)"],"pathways":[{"name":"Propanoate metabolism","kegg_map_id":"00640"},{"name":"Inositol phosphate metabolism","kegg_map_id":"00562"},{"name":"Inositol Metabolism","kegg_map_id":null}],"growth_conditions":[],"references":[{"pubmed_id":18846089,"citation":"Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). \"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.\" Nat Biotechnol 26:1155-1160."},{"pubmed_id":16332871,"citation":"Singh, J., Kumar, D., Ramakrishnan, N., Singhal, V., Jervis, J., Garst, J. F., Slaughter, S. M., DeSantis, A. M., Potts, M., Helm, R. F. (2005). \"Transcriptional response of Saccharomyces cerevisiae to desiccation and rehydration.\" Appl Environ Microbiol 71:8752-8763."}],"proteins":[{"created_at":"2011-05-26T18:22:03.000Z","updated_at":"2011-05-27T15:01:04.000Z","name":"Mitochondrial 2-methylisocitrate lyase","uniprot_id":"Q12031","uniprot_name":"ACEB_YEAST","enzyme":true,"transporter":false,"gene_name":"ICL2","num_residues":575,"molecular_weight":"64975.39844","theoretical_pi":"7.63","general_function":"Involved in isocitrate lyase activity","specific_function":"Catalyzes the formation of pyruvate and succinate from 2-methylisocitrate during the metabolism of endogenous propionyl- CoA. Does not act on isocitrate","reactions":[{"id":1735,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2527,"direction":"\u003e","locations":"Mitochondrion matrix","altext":"(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion matrix","genbank_gene_id":"Z48951","genbank_protein_id":"763005","gene_card_id":"ICL2","chromosome_location":"chromosome 16","locus":"YPR006C","synonyms":["Methylisocitrate lyase"],"enzyme_classes":["4.1.3.30"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxo-acid-lyase activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-carbon lyase activity"},{"category":"Function","description":" isocitrate lyase activity"},{"category":"Process","description":" oxoacid metabolic process"},{"category":"Process","description":" carboxylic acid metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" organic acid metabolic process"}],"pfams":[{"name":"ICL","identifier":"PF00463"}],"pathways":[{"name":"Propanoate metabolism","kegg_map_id":"00640"}],"gene_sequence":"ATGATTACAATGATTAACAACAAAACTTTCAATAGAAAAACTACGGGAACACTGAAGAAGCTGGTTTTGTCATCAGACAAGTCACTGCGAAGATCTTTCAACGGGGCAAGCAGTACTAAAGACTTCGTGTTCTCGGAATCAAGTAAAGTAGAAGAATGGTGGGAATCAGCCAGATTTAAGAATATCAGTCGTCCATACTCAGCTACGGATGTTGTAAAGCATCGGGGCAGCCTTCCTGCTAATACTTCAATTTATCCTTCATCTTATCAAGCTCGAAAGCTGTTCAACTTACTAGAAGAGAATTTCAAGAATGGTACTCCACTTCACACGTTGGGAGTTATCGATCCTGTACAAATGAGTCAGTTGGCCCGTTGCAGAAATATCAAAGTTGCTTACATATCTGGTTGGGCTTGTTCTTCCACATTAGTTGGATCTACAAATGAAGTATCGCCGGATTTTGGCGATTATCCATACGATACTGTGCCGAATCAAGTGGAGAGAATATTCAAGGCGCAGCAATTGCACGATCGAAAGGCTTTCTTGGAGGCCTCCATCAAAGGTTCTACTCCTGTTGATTATTTAAAACCAATTATCGCGGACGCAGACATGGGTCACGGTGGCCCAACGACTGTAATGAAAGTTGCTAAGTTGTTTGCGGAGAAAGGGGCTGCTGGTATTCATCTTGAAGATCAGATGGTGGGAGGCAAAAGGTGTGGCCATCTAAGTGGGGCTGTTTTGGTGCCCACAGCAACACATCTTATGAGATTGATTTCCACCAGGTTTCAATGGGATATCATGGGGACAGAAAATTTGGTTATTGCAAGAACAGATTCCTGTAATGGTAAGCTGTTGAGTTCAAGCAGTGATCCGAGAGACCACGAATTCATTAGGGGTATAATAAGAGATAACGTGGTGCCTTGGAGCGAAAAATTGATTGAGATGGAGGACAAAAAAATTCCCAACTCCGCCATTGCTGACATGGAAAAAGAATGGTACCATGAAAATGAGCTGTTTACATTTGAAGAGGCCTTAGAAAAGCAGTTTACGGCAAGCGAGTTTGAAAGCTATAAAGAAAAGAAGGAAGACCTTATGGTAAACAAGCTGGGTAGAGCATACCTAAGCTTAAGAGAAATGAAACTTTTAGCTCAAGAAGTGACACCACTAAAGAAAATTATATTTGACTGGGATGCTCCGAGGACCAAAGAGGGATATTACATGTTTAACGGTTGTATTGAAGCAGCTATTAGAAGATCTTTGGTGTTTGCCCCATATTCTGATATGATTTGGCTGGAAACGAAAACTCCTGACCTGGAGCAGGCACGCTCATTTTCAAGAAAAATTCATAAACAACTTCCAGCTACCAAGCTAGTATATAACTTATCTCCTAGTTTCAATTGGAGCGCTCACGGCTTTGATGATAAGGCATTAAAATCCTTCGTATGGGACTTGGCAAAAGAAGGCTTCACGTTGCAACTGGTTTCCCTTGCCGGTCTGCATTCAGATGGAGTATCATTCTGGGAATTAGCCAATAGCTTCCAAAGTGACGGAATGAAAGCATACGTCGAAAAAGTGCAAAAACGGGAAAAGGAGACTAATTGTGATATCATGACACACCAGCTATGGTCTGGTGCAGAATATGTTGATTCCTTAATGAAAGTTGTCCAAAACGGTGCTTCATCCCAAACTTTAAGTACATCTGGTGAGAGCTTTACCGAAACGCAATTTTGA","protein_sequence":"MITMINNKTFNRKTTGTLKKLVLSSDKSLRRSFNGASSTKDFVFSESSKVEEWWESARFKNISRPYSATDVVKHRGSLPANTSIYPSSYQARKLFNLLEENFKNGTPLHTLGVIDPVQMSQLARCRNIKVAYISGWACSSTLVGSTNEVSPDFGDYPYDTVPNQVERIFKAQQLHDRKAFLEASIKGSTPVDYLKPIIADADMGHGGPTTVMKVAKLFAEKGAAGIHLEDQMVGGKRCGHLSGAVLVPTATHLMRLISTRFQWDIMGTENLVIARTDSCNGKLLSSSSDPRDHEFIRGIIRDNVVPWSEKLIEMEDKKIPNSAIADMEKEWYHENELFTFEEALEKQFTASEFESYKEKKEDLMVNKLGRAYLSLREMKLLAQEVTPLKKIIFDWDAPRTKEGYYMFNGCIEAAIRRSLVFAPYSDMIWLETKTPDLEQARSFSRKIHKQLPATKLVYNLSPSFNWSAHGFDDKALKSFVWDLAKEGFTLQLVSLAGLHSDGVSFWELANSFQSDGMKAYVEKVQKREKETNCDIMTHQLWSGAEYVDSLMKVVQNGASSQTLSTSGESFTETQF"},{"created_at":"2011-05-27T07:00:12.000Z","updated_at":"2011-07-22T17:53:56.000Z","name":"Probable 2-methylcitrate dehydratase","uniprot_id":"Q12428","uniprot_name":"PRPD_YEAST","enzyme":true,"transporter":false,"gene_name":"PDH1","num_residues":516,"molecular_weight":"57683.10156","theoretical_pi":"9.51","general_function":"Involved in 2-methylcitrate dehydratase activity","specific_function":"Catalyzes the dehydration of 2-methylcitrate to 2- methyl-cis-aconitate","reactions":[{"id":1246,"direction":"\u003c\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2797,"direction":"\u003e","locations":null,"altext":"(2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H(2)O.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"U31900","genbank_protein_id":"939736","gene_card_id":"PDH1","chromosome_location":"chromosome 16","locus":"YPR002W","synonyms":[],"enzyme_classes":["4.2.1.79"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" 2 iron, 2 sulfur cluster binding"},{"category":"Function","description":" 2-methylcitrate dehydratase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" metal cluster binding"},{"category":"Function","description":" iron-sulfur cluster binding"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Process","description":" organic acid metabolic process"},{"category":"Process","description":" oxoacid metabolic process"},{"category":"Process","description":" carboxylic acid metabolic process"},{"category":"Process","description":" monocarboxylic acid metabolic process"},{"category":"Process","description":" propionate metabolic process"},{"category":"Process","description":" propionate catabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" propionate catabolic process, 2-methylcitrate cycle"},{"category":"Process","description":" cellular metabolic process"}],"pfams":[{"name":"MmgE_PrpD","identifier":"PF03972"}],"pathways":[{"name":"Propanoate metabolism","kegg_map_id":"00640"}],"gene_sequence":"ATGTTTTTAGCCAAAAATCTAAAAAATAATAAAATCAAGGTATGCTTGCCTAAAAAGAAATTTGCTGCGCTGAGTACAGCGTCTATACAAACTAATGAAAGACCAAATCCAGATAAGGTTTTGAAGGACATCGCGAAATATGTCCATGAAACCCCATTAAAATCATCTTTGGCTCTAGATACAGCACGACTCTGTTTCCTTGATACTCTAGGCTGTGGCTTGGCGGCTTTGAAATTTAAGCAGGCTCAAAATATTATTAAACCAATTGTGCCAGGAACAATAGTTCCCAGTGGAACAAAAATATTGGGCACATCTTACGTTATGGATCCAGTGAAGGGAGCTTTTGCCATTGGTACTCTAATACGTTGGTTAGATTACAATGACTGCTGGTTAGCTGCCGAGTGGGGGCACCCATCAGATAACCTTGGGGGAATTTTAGCTGTCGCGGATCACTTGTCCAGATTAAACAAGGCTACCCACGGAAAGAATGGAAAACAGTTTCTTGTTAAAGACGTATTAGAGGCAATGATTAAAGCGCATGAAATCCAAGGTATTATAGCGCTCGAAAATTCTTTCAATAAAGTAGGTTTAGATCATGTGGTACTCGTGAAAGTAGCAACGGCTGGTGTTGTCTCGAAGATGCTGGGCCTGAGCCAGGAACAAACTATTGAAGCATTGTCACAAGCATTTGTAGACGGTCAATCACTGCGTACTTACCGTCATGCCCCAAATACTGGATCTAGAAAGTCGTGGGCGGCGGGAGATGCAGTTTCGAGGGCTGTAAACTTGGCTTATTTAGTCAAAAATGCTAATGTTGGCACGATACCTTCAGTATTAACAGCTAGAACCTGGGGATTTTATGACGTTTTATTTAAGGGTAAACCTTTTTCATTCCAACAAAGATCAAAATATGATTCCTACGTCATGGAAAACGTTCTGTTCAAGATATCATTTCCTGCCGAATTCCATGCGCAAACTGCTGTAGAAGCTGCTGTAAAAGCATATAGGATTCTTGCCAAACAAGGGAAAACTTTTAAAGATATTAAATCGATCAGAATTAGAACTCAAGAGGCGGCAATGAGGATTATAGATAAATCCGGTCCTCTGTATAATTATGCCGATAGGGATCATTGTATCCAGTACATGATCGCGGTTCCGCTGATTACTGGTAATCTCACAGCTACTGATTATTCGGATGAGGTCGCAAGAAATCCTGAGATCGATAACTTGAGATCGAAAATGTACTGTATCGAAGATACTCATCTCACTCAAAACTATCACGATCCTGATAAAAGGTCGATAGGAAACGCTCTTCTCATAGAGCTGAACGATGGGACGCAGTTGGATGAAATTTTTGTAGAGTACCCTGTTGGTCACAAATTTAGACGAGAGGAAGGAATACCATTACTAATGAATAAATTTCAAAGGCATCTGCGCGAACATTTTGTAGAGAGCCCTGATAAAGTCGACCTTATAATGAAGGTAAGTTCAAAAACAAACTTTTTGAATATGCAAATCGACAAATACATGGATTTGTTTACTGAGGGATGA","protein_sequence":"MFLAKNLKNNKIKVCLPKKKFAALSTASIQTNERPNPDKVLKDIAKYVHETPLKSSLALDTARLCFLDTLGCGLAALKFKQAQNIIKPIVPGTIVPSGTKILGTSYVMDPVKGAFAIGTLIRWLDYNDCWLAAEWGHPSDNLGGILAVADHLSRLNKATHGKNGKQFLVKDVLEAMIKAHEIQGIIALENSFNKVGLDHVVLVKVATAGVVSKMLGLSQEQTIEALSQAFVDGQSLRTYRHAPNTGSRKSWAAGDAVSRAVNLAYLVKNANVGTIPSVLTARTWGFYDVLFKGKPFSFQQRSKYDSYVMENVLFKISFPAEFHAQTAVEAAVKAYRILAKQGKTFKDIKSIRIRTQEAAMRIIDKSGPLYNYADRDHCIQYMIAVPLITGNLTATDYSDEVARNPEIDNLRSKMYCIEDTHLTQNYHDPDKRSIGNALLIELNDGTQLDEIFVEYPVGHKFRREEGIPLLMNKFQRHLREHFVESPDKVDLIMKVSSKTNFLNMQIDKYMDLFTEG"}]}