{"ymdb_id":"YMDB00403","created_at":"2011-05-29T18:13:23.000Z","updated_at":"2016-09-08T18:35:27.000Z","name":"5-Diphosphomevalonic acid","cas":"4872-34-8","state":"Solid","melting_point":"","description":"5-Diphosphomevalonic acid is an intermediate in the mevalonate pathway used for the synthesis of isopentyl diphosphate (IPP). 5-Diphosphomevalonic acid is formed from 5-phosphomevalonate by the enzyme phosphomevalonate kinase. The mevalonate pathway leads to sterol biosynthesis, ergosterol biosynthesis and dolichol biosynthesis. [Biocyc PWY-922]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":null,"chebi_id":"15899","hmdb_id":"HMDB01090","kegg_id":"C01143","pubchem_id":"516","cs_id":"388531","foodb_id":null,"wikipedia_link":"5-Diphosphomevalonic_acid","biocyc_id":"CPD-641","iupac":"(3R)-3-hydroxy-5-{[hydroxy(phosphonooxy)phosphoryl]oxy}-3-methylpentanoic acid","traditional_iupac":"mevalonate-diphosphate","logp":"-1.638744069","pka":"3.1625026122597153","alogps_solubility":"8.26e+00 g/l","alogps_logp":"-1.17","alogps_logs":"-1.57","acceptor_count":"8","donor_count":"5","rotatable_bond_count":"8","polar_surface_area":"170.82","refractivity":"56.257200000000005","polarizability":"23.46045514564999","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"-2.923623985716116","pka_strongest_acidic":"1.7759296675393568","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(R)-5-Diphosphomevalonate","1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oate","1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid","1,1,3,7-tetrahydroxy-7-methyl-2,4-dioxa-1,3-diphosphanonan-9-oic acid ion(1-)1,3-dioxide","5-diphosphomevalonate","5-diphosphomevalonic acid","mevalonate 5-diphosphate","mevalonate pyrophosphate","mevalonate-diphosphate"],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Cholesterol biosynthesis and metabolism CE(10:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(12:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(14:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(16:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(18:0)","kegg_map_id":null},{"name":"Steroid biosynthesis","kegg_map_id":"00100"}],"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":21062828,"citation":"Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). \"BRENDA, the enzyme information system in 2011.\" Nucleic Acids Res 39:D670-D676."},{"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."}],"proteins":[{"created_at":"2011-05-26T20:25:28.000Z","updated_at":"2011-05-27T15:01:09.000Z","name":"Phosphomevalonate kinase","uniprot_id":"P24521","uniprot_name":"ERG8_YEAST","enzyme":true,"transporter":false,"gene_name":"ERG8","num_residues":451,"molecular_weight":"50454.39844","theoretical_pi":"6.46","general_function":"Involved in ATP binding","specific_function":"ATP + (R)-5-phosphomevalonate = ADP + (R)-5- diphosphomevalonate","reactions":[{"id":1878,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2595,"direction":"\u003e","locations":"Cytoplasm","altext":"ATP + (R)-5-phosphomevalonate = ADP + (R)-5-diphosphomevalonate.","export":false,"pw_reaction_id":null,"source":null},{"id":14370,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006888","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"Z49939","genbank_protein_id":"887601","gene_card_id":"ERG8","chromosome_location":"chromosome 13","locus":"YMR220W","synonyms":[],"enzyme_classes":["2.7.4.2"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" kinase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" phosphorus metabolic process"},{"category":"Process","description":" phosphate metabolic process"},{"category":"Process","description":" phosphorylation"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"GHMP_kinases_C","identifier":"PF08544"},{"name":"GHMP_kinases_N","identifier":"PF00288"}],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Cholesterol biosynthesis and metabolism CE(10:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(12:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(14:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(18:0)","kegg_map_id":null}],"gene_sequence":"ATGTCAGAGTTGAGAGCCTTCAGTGCCCCAGGGAAAGCGTTACTAGCTGGTGGATATTTAGTTTTAGATACAAAATATGAAGCATTTGTAGTCGGATTATCGGCAAGAATGCATGCTGTAGCCCATCCTTACGGTTCATTGCAAGGGTCTGATAAGTTTGAAGTGCGTGTGAAAAGTAAACAATTTAAAGATGGGGAGTGGCTGTACCATATAAGTCCTAAAAGTGGCTTCATTCCTGTTTCGATAGGCGGATCTAAGAACCCTTTCATTGAAAAAGTTATCGCTAACGTATTTAGCTACTTTAAACCTAACATGGACGACTACTGCAATAGAAACTTGTTCGTTATTGATATTTTCTCTGATGATGCCTACCATTCTCAGGAGGATAGCGTTACCGAACATCGTGGCAACAGAAGATTGAGTTTTCATTCGCACAGAATTGAAGAAGTTCCCAAAACAGGGCTGGGCTCCTCGGCAGGTTTAGTCACAGTTTTAACTACAGCTTTGGCCTCCTTTTTTGTATCGGACCTGGAAAATAATGTAGACAAATATAGAGAAGTTATTCATAATTTAGCACAAGTTGCTCATTGTCAAGCTCAGGGTAAAATTGGAAGCGGGTTTGATGTAGCGGCGGCAGCATATGGATCTATCAGATATAGAAGATTCCCACCCGCATTAATCTCTAATTTGCCAGATATTGGAAGTGCTACTTACGGCAGTAAACTGGCGCATTTGGTTGATGAAGAAGACTGGAATATTACGATTAAAAGTAACCATTTACCTTCGGGATTAACTTTATGGATGGGCGATATTAAGAATGGTTCAGAAACAGTAAAACTGGTCCAGAAGGTAAAAAATTGGTATGATTCGCATATGCCAGAAAGCTTGAAAATATATACAGAACTCGATCATGCAAATTCTAGATTTATGGATGGACTATCTAAACTAGATCGCTTACACGAGACTCATGACGATTACAGCGATCAGATATTTGAGTCTCTTGAGAGGAATGACTGTACCTGTCAAAAGTATCCTGAAATCACAGAAGTTAGAGATGCAGTTGCCACAATTAGACGTTCCTTTAGAAAAATAACTAAAGAATCTGGTGCCGATATCGAACCTCCCGTACAAACTAGCTTATTGGATGATTGCCAGACCTTAAAAGGAGTTCTTACTTGCTTAATACCTGGTGCTGGTGGTTATGACGCCATTGCAGTGATTACTAAGCAAGATGTTGATCTTAGGGCTCAAACCGCTAATGACAAAAGATTTTCTAAGGTTCAATGGCTGGATGTAACTCAGGCTGACTGGGGTGTTAGGAAAGAAAAAGATCCGGAAACTTATCTTGATAAATAA","protein_sequence":"MSELRAFSAPGKALLAGGYLVLDTKYEAFVVGLSARMHAVAHPYGSLQGSDKFEVRVKSKQFKDGEWLYHISPKSGFIPVSIGGSKNPFIEKVIANVFSYFKPNMDDYCNRNLFVIDIFSDDAYHSQEDSVTEHRGNRRLSFHSHRIEEVPKTGLGSSAGLVTVLTTALASFFVSDLENNVDKYREVIHNLAQVAHCQAQGKIGSGFDVAAAAYGSIRYRRFPPALISNLPDIGSATYGSKLAHLVDEEDWNITIKSNHLPSGLTLWMGDIKNGSETVKLVQKVKNWYDSHMPESLKIYTELDHANSRFMDGLSKLDRLHETHDDYSDQIFESLERNDCTCQKYPEITEVRDAVATIRRSFRKITKESGADIEPPVQTSLLDDCQTLKGVLTCLIPGAGGYDAIAVITKQDVDLRAQTANDKRFSKVQWLDVTQADWGVRKEKDPETYLDK"},{"created_at":"2011-05-26T20:46:41.000Z","updated_at":"2011-05-27T15:01:09.000Z","name":"Diphosphomevalonate decarboxylase","uniprot_id":"P32377","uniprot_name":"MVD1_YEAST","enzyme":true,"transporter":false,"gene_name":"MVD1","num_residues":396,"molecular_weight":"44115.5","theoretical_pi":"5.49","general_function":"Involved in ATP binding","specific_function":"ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)","reactions":[{"id":1740,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2600,"direction":"\u003e","locations":null,"altext":"ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2).","export":false,"pw_reaction_id":null,"source":null},{"id":14371,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006889","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1FI4","cellular_location":null,"genbank_gene_id":"AY693152","genbank_protein_id":"51013755","gene_card_id":"MVD1","chromosome_location":"chromosome 14","locus":"YNR043W","synonyms":["Ergosterol biosynthesis protein 19","Mevalonate pyrophosphate decarboxylase","Mevalonate-5-diphosphate decarboxylase","MDD","MDDase"],"enzyme_classes":["4.1.1.33"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-carbon lyase activity"},{"category":"Function","description":" carboxy-lyase activity"},{"category":"Function","description":" diphosphomevalonate decarboxylase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" nucleoside binding"},{"category":"Function","description":" purine nucleoside binding"},{"category":"Function","description":" adenyl nucleotide binding"},{"category":"Function","description":" adenyl ribonucleotide binding"},{"category":"Function","description":" ATP binding"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" kinase activity"},{"category":"Function","description":" transferase activity"},{"category":"Process","description":" phosphorylation"},{"category":"Process","description":" lipid metabolic process"},{"category":"Process","description":" cellular lipid metabolic process"},{"category":"Process","description":" isoprenoid metabolic process"},{"category":"Process","description":" isoprenoid biosynthetic process"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" primary metabolic process"},{"category":"Process","description":" phosphorus metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" phosphate metabolic process"}],"pfams":[{"name":"GHMP_kinases_N","identifier":"PF00288"}],"pathways":[{"name":"Terpenoid backbone biosynthesis","kegg_map_id":"00900"},{"name":"Cholesterol biosynthesis and metabolism CE(10:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(12:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(14:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(16:0)","kegg_map_id":null},{"name":"Cholesterol biosynthesis and metabolism CE(18:0)","kegg_map_id":null}],"gene_sequence":"ATGACCGTTTACACAGCATCCGTTACCGCACCCGTCAACATCGCAACCCTTAAGTATTGGGGGAAAAGGGACACGAAGTTGAATCTGCCCACCAATTCGTCCATATCAGTGACTTTATCGCAAGATGACCTCAGAACGTTGACCTCTGCGGCTACTGCACCTGAGTTTGAACGCGACACTTTGTGGTTAAATGGAGAACCACACAGCATCGACAATGAAAGAACTCAAAATTGTCTGCGCGACCTACGCCAATTAAGAAAGGAAATGGAATCGAAGGACGCCTCATTGCCCACATTATCTCAATGGAAACTCCACATTGTCTCCGAAAATAACTTTCCTACAGCAGCTGGTTTAGCTTCCTCCGCTGCTGGCTTTGCTGCATTGGTCTCTGCAATTGCTAAGTTATACCAATTACCACAGTCAACTTCAGAAATATCTAGAATAGCAAGAAAGGGGTCTGGTTCAGCTTGTAGATCGTCGTTTGGCGGATACGTGGCCTGGGAAATGGGAAAAGCTGAAGATGGTCATGATTCCATGGCAGTACAAATCGCAGACAGCTCTGACTGGCCTCAGATGAAAGCTTGTGTCCTAGTTGTCAGCGATATTAAAAAGGATGTGAGTTCCACTCAGGGTATGCAATTGACCGTGGCAACCTCCGAACTATTTAAAGAAAGAATTGAACATGTCGTACCAAAGAGATTTGAAGTCATGCGTAAAGCCATTGTTGAAAAAGATTTCGCCACCTTTGCAAAGGAAACAATGATGGATTCCAACTCTTTCCATGCCACATGTTTGGACTCTTTCCCTCCAATATTCTACATGAATGACACTTCCAAGCGTATCATCAGTTGGTGCCACACCATTAATCAGTTTTACGGAGAAACAATCGTTGCATACACGTTTGATGCAGGTCCAAATGCTGTGTTGTACTACTTAGCTGAAAATGAGTCGAAACTCTTTGCATTTATCTATAAATTGTTTGGCTCTGTTCCTGGATGGGACAAGAAATTTACTACTGAGCAGCTTGAGGCTTTCAACCATCAATTTGAATCATCTAACTTTACTGCACGTGAATTGGATCTTGAGTTGCAAAAGGATGTTGCCAGAGTGATTTTAACTCAAGTCGGTTCAGGCCCACAAGAAACAAACGAATCTTTGATTGACGCAAAGACTGGTCTACCAAAGGAATAA","protein_sequence":"MTVYTASVTAPVNIATLKYWGKRDTKLNLPTNSSISVTLSQDDLRTLTSAATAPEFERDTLWLNGEPHSIDNERTQNCLRDLRQLRKEMESKDASLPTLSQWKLHIVSENNFPTAAGLASSAAGFAALVSAIAKLYQLPQSTSEISRIARKGSGSACRSLFGGYVAWEMGKAEDGHDSMAVQIADSSDWPQMKACVLVVSDIKKDVSSTQGMQLTVATSELFKERIEHVVPKRFEVMRKAIVEKDFATFAKETMMDSNSFHATCLDSFPPIFYMNDTSKRIISWCHTINQFYGETIVAYTFDAGPNAVLYYLAENESKLFAFIYKLFGSVPGWDKKFTTEQLEAFNHQFESSNFTARELDLELQKDVARVILTQVGSGPQETNESLIDAKTGLPKE"}]}