{"ymdb_id":"YMDB00068","created_at":"2011-05-29T15:53:40.000Z","updated_at":"2016-09-08T18:34:58.000Z","name":"(R)-2,3-Dihydroxy-3-methylvalerate","cas":"562-43-6","state":"Solid","melting_point":"","description":"(R)-2,3-Dihydroxy-methylvalerate is an intermediate in valine, leucine and isoleucine biosynthesis.","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"Mitochondrion","synthesis_reference":null,"chebi_id":"27512","hmdb_id":"HMDB12140","kegg_id":"C06007","pubchem_id":"448154","cs_id":null,"foodb_id":null,"wikipedia_link":null,"biocyc_id":"1-KETO-2-METHYLVALERATE","iupac":"(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid","traditional_iupac":"(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid","logp":"-0.2990653966666666","pka":"13.109092933547867","alogps_solubility":"4.86e+02 g/l","alogps_logp":"-0.44","alogps_logs":"0.52","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"3","polar_surface_area":"77.75999999999999","refractivity":"33.9645","polarizability":"14.433750785635485","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"-3.320314291594766","pka_strongest_acidic":"3.930562552523404","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2R,3R)-2,3-dihydroxy-3-methylpentanoate","(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid","(2R,3R)-2,3-dihydroxy-3-methylvalerate","(R)-2,3-Dihydroxy-3-methylpentanoate","(R)-2,3-Dihydroxy-3-methylpentanoic acid","(R)-2,3-Dihydroxy-3-methylvalerate","1-keto-2-methylvalerate","2,3-Dihydroxy-3-Methyl-Valeric acid","2,3-Dihydroxy-3-methylpentanoate","2,3-Dihydroxy-3-methylpentanoic acid","2,3-Dihydroxy-Valerianic acid","4,5-dideoxy-3-C-methyl-pentonic acid","Alpha,beta-dihydroxy-beta-methylvaleric acid","CID8","DMV"],"pathways":[{"name":"Valine, leucine and isoleucine biosynthesis","kegg_map_id":"00290"},{"name":"isoleucine biosynthesis","kegg_map_id":null}],"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":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":4616942,"citation":"Ryan, E. D., Kohlhaw, G. B. (1974). \"Subcellular localization of isoleucine-valine biosynthetic enzymes in yeast.\" J Bacteriol 120:631-637."}],"proteins":[{"created_at":"2011-05-24T21:09:37.000Z","updated_at":"2011-07-22T17:53:52.000Z","name":"Ketol-acid reductoisomerase, mitochondrial","uniprot_id":"P06168","uniprot_name":"ILV5_YEAST","enzyme":true,"transporter":false,"gene_name":"ILV5","num_residues":395,"molecular_weight":"44368.10156","theoretical_pi":"9.42","general_function":"Involved in oxidoreductase activity","specific_function":"(R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH","reactions":[{"id":1142,"direction":"\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1229,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1682,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2362,"direction":"\u003e","locations":"Mitochondrion","altext":"(R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":2363,"direction":"\u003e","locations":"Mitochondrion","altext":"(2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-hydroxy-2-ethyl-3-oxobutanoate + NADPH.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"U19102","genbank_protein_id":"609403","gene_card_id":"ILV5","chromosome_location":"chromosome 12","locus":"YLR355C","synonyms":["Acetohydroxy-acid reductoisomerase","Alpha-keto-beta-hydroxylacil reductoisomerase"],"enzyme_classes":["1.1.1.86"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" 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":" coenzyme binding"},{"category":"Function","description":" ketol-acid reductoisomerase activity"},{"category":"Process","description":" branched chain family amino acid biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" cellular amino acid biosynthetic process"}],"pfams":[{"name":"IlvC","identifier":"PF01450"},{"name":"IlvN","identifier":"PF07991"}],"pathways":[{"name":"Valine, leucine and isoleucine biosynthesis","kegg_map_id":"00290"},{"name":"Pantothenate and CoA 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dehydratase, mitochondrial","uniprot_id":"P39522","uniprot_name":"ILV3_YEAST","enzyme":true,"transporter":false,"gene_name":"ILV3","num_residues":585,"molecular_weight":"62860.60156","theoretical_pi":"7.92","general_function":"Involved in metabolic process","specific_function":"2,3-dihydroxy-3-methylbutanoate = 3-methyl-2- oxobutanoate + H(2)O","reactions":[{"id":1463,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1464,"direction":"\u003e","locations":"mitochondrion","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2772,"direction":"\u003e","locations":"Mitochondrion","altext":"2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H(2)O.","export":false,"pw_reaction_id":null,"source":null},{"id":14224,"direction":"\u003c\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006662","source":"Smpdb"},{"id":14225,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006762","source":"Smpdb"},{"id":14226,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006772","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Mitochondrion","genbank_gene_id":"X87611","genbank_protein_id":"854590","gene_card_id":"ILV3","chromosome_location":"chromosome 10","locus":"YJR016C","synonyms":["DAD","2,3-dihydroxy acid hydrolyase"],"enzyme_classes":["4.2.1.9"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Function","description":" dihydroxy-acid dehydratase activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"},{"category":"Process","description":" cellular amino acid biosynthetic process"},{"category":"Process","description":" branched chain family amino acid biosynthetic process"}],"pfams":[{"name":"ILVD_EDD","identifier":"PF00920"}],"pathways":[{"name":"Valine, leucine and isoleucine biosynthesis","kegg_map_id":"00290"},{"name":"Pantothenate and CoA 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2-reductase","uniprot_id":"P38787","uniprot_name":"PANE_YEAST","enzyme":true,"transporter":false,"gene_name":"PAN5","num_residues":379,"molecular_weight":"42820.89844","theoretical_pi":"6.62","general_function":"Involved in oxidoreductase activity","specific_function":"Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid","reactions":[{"id":1142,"direction":"\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2839,"direction":"\u003e","locations":null,"altext":"(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH.","export":false,"pw_reaction_id":null,"source":null},{"id":14216,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006655","source":"Smpdb"},{"id":14217,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006763","source":"Smpdb"},{"id":14218,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006771","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":"PAN5","chromosome_location":"chromosome 8","locus":"YHR063C","synonyms":["Ketopantoate reductase","KPA reductase","KPR"],"enzyme_classes":["1.1.1.169"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" coenzyme binding"},{"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":" NADP or NADPH binding"},{"category":"Process","description":" pantothenate biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" cofactor metabolic process"},{"category":"Process","description":" coenzyme metabolic process"},{"category":"Process","description":" coenzyme biosynthetic process"}],"pfams":[{"name":"ApbA","identifier":"PF02558"},{"name":"ApbA_C","identifier":"PF08546"}],"pathways":[{"name":"Pantothenate and CoA biosynthesis","kegg_map_id":"00770"}],"gene_sequence":"ATGACTGCACCACACAGAAGTACTATTCATATTCTTGGGTTGGGTGCCATGGGTACCGTTTTGGCAGTTGACCTTTTAAGATTTACCAATGCCCTAGTTGTGCCCTTATTTAGATCACAAGAAAGACTTGCACAATTTCAGAAGACAAATGGGAACAACATTTCGATTCGCAAACTTTATTTGGAAGGCTCGCCAATATTTTCTTATCCAGTGGAGAAATGCGAATGCCCTGAAACTTTCTCTAAAAAACCTATTGACAACTTAGTCGTCACTACAAAGACTTACCAAACCAAAGAAGCACTAGCTCCTTATTTGCCTTATATTAATAAAAATACAAACTTAATTTTGATTCAGAATGGACTGGGCGTTTTAGAACTATTGAGAGAAGAAATCTTTACAGATTCAAAAAACAGACCACATTTATTTCAGGGTGTCATTTCTCATGGCGTTTATCAGGATAAAGCAGGAGTTTTCAATCATGCTGGGTGGGCTGGTATGAAAATTGCCAAATTGCCTTGGACTGAGGAAGAAATGATTCAAAAAAAATCCGTAGTCGAGGACGATGCAGCCAATAACTCATTAGTAAAATTATTAACAGAACCAAAATTTGCCAAGGAATTTGGAATAGAACATTCCACTTATCAAGAAATGCTCTTTGGTCAATTATTTAAATTTTTGGTTAATGCATGCATGAATCCAGTTACGGCTATTCTAGATTGTGTCAATGGTGAGATGAAGGCCAGTTGCGGTCCAGTTTTCACATCTATTATTGACGAGTGTTTACAAATATTGAGAGTTGCTTATAGGCCATTGTTTCAATACCACGAAAAATACAGCGGTAATGAAGAATACCCAGAAATGGATGTCAATGCAGTACTGACAACCGATAACATGGTCTCCGAAGTCACTAGAATTGGCTGTGACATCAATTCTAGGAACAGTAGTTCAATGAGACAAGACACTTTGTTCTTAAGAGACATTGAAATTGAGTATATCAATGGCTATGTCGTCAAATTGGCTGATAACTTAAATCTAGACCCAAACTGCTGCAAGGTTAATAAAACTATCGGAGAATTGGCCACTATGAGATTAGCATTGAACAGGTCGAGAAGTATCAATGGTGACTGGAGAAAGGACTGA","protein_sequence":"MTAPHRSTIHILGLGAMGTVLAVDLLRFTNALVVPLFRSQERLAQFQKTNGNNISIRKLYLEGSPIFSYPVEKCECPETFSKKPIDNLVVTTKTYQTKEALAPYLPYINKNTNLILIQNGLGVLELLREEIFTDSKNRPHLFQGVISHGVYQDKAGVFNHAGWAGMKIAKLPWTEEEMIQKKSVVEDDAANNSLVKLLTEPKFAKEFGIEHSTYQEMLFGQLFKFLVNACMNPVTAILDCVNGEMKASCGPVFTSIIDECLQILRVAYRPLFQYHEKYSGNEEYPEMDVNAVLTTDNMVSEVTRIGCDINSRNSSSMRQDTLFLRDIEIEYINGYVVKLADNLNLDPNCCKVNKTIGELATMRLALNRSRSINGDWRKD"}]}