{"ymdb_id":"YMDB00059","created_at":"2011-05-29T15:52:50.000Z","updated_at":"2016-09-08T18:34:57.000Z","name":"2-hydroxyglutaric acid","cas":"2889-31-8","state":"Solid","melting_point":"\u003e300 oC","description":"alpha-Hydroxyglutaric acid (2-hydroxyglutaric acid) is an alpha hydroxy acid. 2-hydroxyglutarate is formed from glutamate and can be converted to 2-oxogluterate a key Krebb cycle intermediate. The formation of 2-hydroxyglutarate may act as a local sink for NADH. [PMID: 9639938]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":null,"synthesis_reference":"Kobayashi, Hidehiko; Yamaguchi, Koretaka; Yamashita, Takeshi.  a-Hydroxyglutaric acid from glutamic acid.    Jpn. Tokkyo Koho  (1968),     3 pp. ","chebi_id":"32796","hmdb_id":"HMDB00606","kegg_id":"C01087","pubchem_id":"43","cs_id":"42","foodb_id":null,"wikipedia_link":"Alpha-Hydroxyglutaric_acid","biocyc_id":null,"iupac":"2-hydroxypentanedioic acid","traditional_iupac":"2-hydroxyglutaric acid","logp":"-0.824980223","pka":"4.159324461588801","alogps_solubility":"1.57e+02 g/l","alogps_logp":"-1.04","alogps_logs":"0.03","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"4","polar_surface_area":"94.83000000000001","refractivity":"29.6302","polarizability":"12.97429694878232","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.8068384384876675","pka_strongest_acidic":"3.276485914460605","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(R)-2-hydroxy-Pentanedioate","(R)-2-hydroxy-Pentanedioic acid","(R)-2-Hydroxyglutarate","(R)-2-Hydroxyglutaric acid","(R)-2-hydroxypentanedioic acid","(R)-a-Hydroxyglutarate","(R)-a-Hydroxyglutaric acid","(R)-alpha-Hydroxyglutarate","(R)-alpha-Hydroxyglutaric acid","(R)-Hydroxyglutarate","2-hydroxy-D-Glutarate","2-hydroxy-D-Glutaric acid","2-hydroxy-delta-Glutarate","2-hydroxy-delta-Glutaric acid","D-2-Hydroxyglutarate","D-2-Hydroxyglutaric acid","D-a-Hydroxyglutarate","D-a-Hydroxyglutaric acid","delta-2-Hydroxyglutarate","delta-2-Hydroxyglutaric acid","delta-alpha-Hydroxyglutarate","delta-alpha-Hydroxyglutaric acid","R-2-HYDROXYGLUTARATE"],"pathways":[],"growth_conditions":[],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"pubmed_id":9639938,"citation":"Albers, E., Gustafsson, L., Niklasson, C., Liden, G. (1998). \"Distribution of 14C-labelled carbon from glucose and glutamate during anaerobic growth of Saccharomyces cerevisiae.\" Microbiology 144 ( Pt 6):1683-1690."},{"pubmed_id":17439666,"citation":"Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., Rash, B., Brown, M., Dunn, W. B., Broadhurst, D., O'Donoghue, K., Hester, S. S., Dunkley, T. P., Hart, S. R., Swainston, N., Li, P., Gaskell, S. J., Paton, N. W., Lilley, K. S., Kell, D. B., Oliver, S. G. (2007). \"Growth control of the eukaryote cell: a systems biology study in yeast.\" J Biol 6:4."}],"proteins":[{"created_at":"2011-05-26T16:51:54.000Z","updated_at":"2011-05-27T15:01:01.000Z","name":"D-3-phosphoglycerate dehydrogenase 2","uniprot_id":"P40510","uniprot_name":"SER33_YEAST","enzyme":true,"transporter":false,"gene_name":"SER33","num_residues":469,"molecular_weight":"51187.80078","theoretical_pi":"6.38","general_function":"Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor","specific_function":"3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH","reactions":[{"id":1866,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2448,"direction":"\u003e","locations":"","altext":"3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":2449,"direction":"\u003e","locations":"","altext":"2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":3841,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006364","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"Z37997","genbank_protein_id":"556873","gene_card_id":"SER33","chromosome_location":"chromosome 9","locus":"YIL074C","synonyms":["3-PGDH 2"],"enzyme_classes":["1.1.1.95"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleotide binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" NAD or NADH binding"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"2-Hacid_dh","identifier":"PF00389"},{"name":"2-Hacid_dh_C","identifier":"PF02826"}],"pathways":[{"name":"Glycine, serine and threonine metabolism","kegg_map_id":"00260"},{"name":"Methane metabolism","kegg_map_id":"00680"},{"name":"glycine metabolism","kegg_map_id":null},{"name":"serine metabolism","kegg_map_id":null}],"gene_sequence":"ATGTCTTATTCAGCTGCCGATAATTTACAAGATTCATTCCAACGTGCCATGAACTTTTCTGGCTCTCCTGGTGCAGTCTCAACCTCACCAACTCAGTCATTTATGAACACACTACCTCGTCGTGTAAGCATTACAAAGCAACCAAAGGCTTTAAAACCTTTTTCTACTGGTGACATGAATATTCTACTGTTGGAAAATGTCAATGCAACTGCAATCAAAATCTTCAAGGATCAGGGTTACCAAGTAGAGTTCCACAAGTCTTCTCTACCTGAGGATGAATTGATTGAAAAAATCAAAGACGTACACGCTATCGGTATAAGATCCAAAACTAGATTGACTGAAAAAATACTACAGCATGCCAGGAATCTAGTTTGTATTGGTTGTTTTTGCATAGGTACCAATCAAGTAGACCTAAAATATGCCGCTAGTAAAGGTATTGCTGTTTTCAATTCGCCATTCTCCAATTCAAGATCCGTAGCAGAATTGGTAATTGGTGAGATCATTAGTTTAGCAAGACAATTAGGTGATAGATCCATTGAACTGCATACAGGTACATGGAATAAAGTCGCTGCTAGGTGTTGGGAAGTAAGAGGAAAAACTCTCGGTATTATTGGGTATGGTCACATTGGTTCGCAATTATCAGTTCTTGCAGAAGCTATGGGCCTGCATGTGCTATACTATGATATCGTGACAATTATGGCCTTAGGTACTGCCAGACAAGTTTCTACATTAGATGAATTGTTGAATAAATCTGATTTTGTAACACTACATGTACCAGCTACTCCAGAAACTGAAAAAATGTTATCTGCTCCACAATTCGCTGCTATGAAGGACGGGGCTTATGTTATTAATGCCTCAAGAGGTACTGTCGTGGACATTCCATCTCTGATCCAAGCCGTCAAGGCCAACAAAATTGCAGGTGCTGCTTTAGATGTTTATCCACATGAACCAGCTAAGAACGGTGAAGGTTCATTTAACGATGAACTTAACAGCTGGACTTCTGAGTTGGTTTCATTACCAAATATAATCCTGACACCACATATTGGTGGCTCTACAGAAGAAGCTCAAAGTTCAATCGGTATTGAGGTGGCTACTGCATTGTCCAAATACATCAATGAAGGTAACTCTGTCGGTTCTGTGAACTTCCCAGAAGTCAGTTTGAAGTCTTTGGACTACGATCAAGAGAACACAGTACGTGTCTTGTATATTCATCGTAACGTTCCTGGTGTTTTGAAGACCGTTAATGATATCTTATCCGATCATAATATCGAGAAACAGTTTTCTGATTCTCACGGCGAGATCGCTTATCTAATGGCAGACATCTCTTCTGTTAATCAAAGTGAAATCAAGGATATATATGAAAAGTTGAACCAAACTTCTGCCAAAGTTTCCATCAGGTTATTATACTAA","protein_sequence":"MSYSAADNLQDSFQRAMNFSGSPGAVSTSPTQSFMNTLPRRVSITKQPKALKPFSTGDMNILLLENVNATAIKIFKDQGYQVEFHKSSLPEDELIEKIKDVHAIGIRSKTRLTEKILQHARNLVCIGCFCIGTNQVDLKYAASKGIAVFNSPFSNSRSVAELVIGEIISLARQLGDRSIELHTGTWNKVAARCWEVRGKTLGIIGYGHIGSQLSVLAEAMGLHVLYYDIVTIMALGTARQVSTLDELLNKSDFVTLHVPATPETEKMLSAPQFAAMKDGAYVINASRGTVVDIPSLIQAVKANKIAGAALDVYPHEPAKNGEGSFNDELNSWTSELVSLPNIILTPHIGGSTEEAQSSIGIEVATALSKYINEGNSVGSVNFPEVSLKSLDYDQENTVRVLYIHRNVPGVLKTVNDILSDHNIEKQFSDSHGEIAYLMADISSVNQSEIKDIYEKLNQTSAKVSIRLLY"},{"created_at":"2011-05-27T17:20:48.000Z","updated_at":"2011-05-29T05:06:52.000Z","name":"D-3-phosphoglycerate dehydrogenase 1","uniprot_id":"P40054","uniprot_name":"SERA_YEAST","enzyme":true,"transporter":false,"gene_name":"SER3","num_residues":469,"molecular_weight":"51192.80078","theoretical_pi":"5.28","general_function":"Involved in oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor","specific_function":"3-phospho-D-glycerate + NAD(+) = 3- phosphonooxypyruvate + NADH","reactions":[{"id":1866,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2448,"direction":"\u003e","locations":"","altext":"3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":2449,"direction":"\u003e","locations":"","altext":"2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH.","export":false,"pw_reaction_id":null,"source":null},{"id":3841,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006364","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":null,"genbank_protein_id":null,"gene_card_id":"SER3","chromosome_location":"chromosome 5","locus":"YER081W","synonyms":["3-PGDH 1"],"enzyme_classes":["1.1.1.95"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleotide binding"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" cofactor binding"},{"category":"Function","description":" oxidoreductase activity, acting on CH-OH group of donors"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor"},{"category":"Function","description":" NAD or NADH binding"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"2-Hacid_dh","identifier":"PF00389"},{"name":"2-Hacid_dh_C","identifier":"PF02826"}],"pathways":[{"name":"Glycine, serine and threonine metabolism","kegg_map_id":"00260"},{"name":"Methane metabolism","kegg_map_id":"00680"},{"name":"glycine metabolism","kegg_map_id":null},{"name":"serine metabolism","kegg_map_id":null}],"gene_sequence":"ATGACAAGCATTGACATTAACAACTTACAAAATACCTTTCAACAAGCTATGAATATGAGCGGCTCCCCAGGCGCTGTTTGTACTTCACCTACGCAATCTTTCATGAATACCGTTCCACAGCGCTTGAATGCTGTAAAGCACCCAAAAATTTTGAAGCCTTTCTCAACGGGTGATATGAAGATTTTACTATTAGAAAACGTTAATCAAACTGCTATTACAATCTTCGAAGAGCAAGGTTACCAAGTCGAATTCTATAAATCTTCATTGCCCGAGGAAGAGTTGATCGAAAAGATCAAGGACGTTCATGCTATTGGTATCAGATCAAAGACTAGATTAACTTCAAATGTCTTACAACATGCGAAGAATCTGGTTTGTATTGGTTGTTTCTGTATCGGTACCAACCAAGTTGACTTAGACTACGCTACCAGCAGAGGTATTGCTGTTTTCAACTCGCCTTTCTCCAACTCAAGATCAGTAGCAGAATTGGTCATCGCTGAAATCATTAGTTTAGCAAGACAACTAGGTGATAGATCTATCGAATTACATACCGGTACATGGAATAAGGTTGCTGCTAGATGTTGGGAGGTAAGAGGAAAAACTCTTGGTATTATTGGGTACGGTCACATTGGTTCCCAATTATCAGTTCTTGCAGAAGCTATGGGTTTGCATGTGTTGTACTACGATATTGTAACTATCATGGCCTTGGGTACTGCCAGACAAGTTTCTACATTAGATGAATTGTTGAATAAATCTGATTTTGTGACACTACATGTACCAGCTACTCCTGAAACTGAAAAAATGTTATCTGCCCCACAATTTGCTGCTATGAAGGATGGCGCTTATGTTATTAATGCTTCAAGAGGTACTGTCGTGGACATTCCATCTTTGATCCAAGCCGTGAAAGCCAACAAAATTGCAGGTGCTGCTTTGGATGTTTATCCACATGAACCAGCTAAGAACGGTGAAGGTTCATTTAACGATGAGCTAAATAGCTGGACTTCTGAATTAGTTTCATTACCAAATATCATCTTGACACCACACATTGGTGGCTCTACCGAAGAAGCCCAAAGCTCAATCGGTATTGAAGTGGCTACCGCATTGTCCAAATACATCAATGAAGGTAACTCTGTCGGTTCAGTCAACTTCCCAGAAGTGGCATTGAAATCATTGTCTTACGACCAAGAGAACACTGTGCGTGTGTTATACATTCACCAAAATGTACCAGGTGTTTTGAAGACCGTCAATGATATTTTATCGAACCATAACATCGAAAAGCAATTTTCCGATTCAAATGGTGAAATTGCTTATTTAATGGCTGATATCTCTTCTGTTGACCAAAGCGATATTAAAGATATTTATGAACAACTAAATCAAACCTCTGCTAAGATCTCAATTAGATTGCTATATTAA","protein_sequence":"MTSIDINNLQNTFQQAMNMSGSPGAVCTSPTQSFMNTVPQRLNAVKHPKILKPFSTGDMKILLLENVNQTAITIFEEQGYQVEFYKSSLPEEELIEKIKDVHAIGIRSKTRLTSNVLQHAKNLVCIGCFCIGTNQVDLDYATSRGIAVFNSPFSNSRSVAELVIAEIISLARQLGDRSIELHTGTWNKVAARCWEVRGKTLGIIGYGHIGSQLSVLAEAMGLHVLYYDIVTIMALGTARQVSTLDELLNKSDFVTLHVPATPETEKMLSAPQFAAMKDGAYVINASRGTVVDIPSLIQAVKANKIAGAALDVYPHEPAKNGEGSFNDELNSWTSELVSLPNIILTPHIGGSTEEAQSSIGIEVATALSKYINEGNSVGSVNFPEVALKSLSYDQENTVRVLYIHQNVPGVLKTVNDILSNHNIEKQFSDSNGEIAYLMADISSVDQSDIKDIYEQLNQTSAKISIRLLY"}]}