{"ymdb_id":"YMDB00024","created_at":"2011-05-29T15:49:28.000Z","updated_at":"2016-09-08T18:34:55.000Z","name":"5-(methylsulfanyl)-2,3-dioxopentyl phosphate","cas":null,"state":null,"melting_point":null,"description":"5-(Methylsulfanyl)-2,3-dioxopentyl phosphate is an intermediate in the S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation pathway. [Biocyc PWY-6755]","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"cytoplasm","synthesis_reference":null,"chebi_id":"50604","hmdb_id":null,"kegg_id":"C15650","pubchem_id":"561","cs_id":"545","foodb_id":null,"wikipedia_link":null,"biocyc_id":"CPD-8999","iupac":"{[5-(methylsulfanyl)-2,3-dioxopentyl]oxy}phosphonic acid","traditional_iupac":"1-pdmsp","logp":"0.5128286950000003","pka":"6.143880429984992","alogps_solubility":"7.99e+00 g/l","alogps_logp":"-0.08","alogps_logs":"-1.48","acceptor_count":"5","donor_count":"2","rotatable_bond_count":"7","polar_surface_area":"100.9","refractivity":"51.197100000000006","polarizability":"21.009206917920018","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-9.360354692322906","pka_strongest_acidic":"1.1140333449772122","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"1","veber_rule":"0","mddr_like_rule":"0","synonyms":["1-PDMSP","1-Phospho-2,3-diketo-5-S-methylthiopentane","2,3-diketo-5-methylthio-1-phosphopentane","2,3-Diketo-5-methylthiopentyl-1-phosphate","2,3-diketo-5-Methylthiopentyl-1-phosphoric acid","5-(Methylthio)-2,3-dioxopentyl phosphate","5-(methylthio)-2,3-Dioxopentyl phosphoric acid","5-methylthio-1-(phosphonooxy)pentane-2,3-dione"],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","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":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."},{"pubmed_id":14506228,"citation":"Subhi, A. L., Diegelman, P., Porter, C. W., Tang, B., Lu, Z. J., Markham, G. D., Kruger, W. D. (2003). \"Methylthioadenosine phosphorylase regulates ornithine decarboxylase by production of downstream metabolites.\" J Biol Chem 278:49868-49873."}],"proteins":[{"created_at":"2011-05-24T20:34:21.000Z","updated_at":"2011-05-29T14:01:21.000Z","name":"Enolase-phosphatase E1","uniprot_id":"P32626","uniprot_name":"ENOPH_YEAST","enzyme":true,"transporter":false,"gene_name":"UTR4","num_residues":227,"molecular_weight":"25187.19922","theoretical_pi":"5.3","general_function":"Involved in catalytic activity","specific_function":"Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene)","reactions":[{"id":2327,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":2328,"direction":"\u003e","locations":"Cytoplasmic;Cytoplasm. Nucleus","altext":"2-Phosphoglycolate + H2O = glycolate + phosphate","export":false,"pw_reaction_id":null,"source":null},{"id":3792,"direction":null,"locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006311","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"U18779","genbank_protein_id":"603641","gene_card_id":"UTR4","chromosome_location":"chromosome 5","locus":"YEL038W","synonyms":["2,3-diketo-5-methylthio-1-phosphopentane phosphatase","Unknown transcript 4 protein"],"enzyme_classes":["3.1.3.77","3.1.3.18"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" acireductone synthase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on ester bonds"},{"category":"Function","description":" phosphoric ester hydrolase activity"},{"category":"Function","description":" phosphatase activity"},{"category":"Function","description":" phosphoglycolate phosphatase activity"},{"category":"Process","description":" cellular amino acid biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" amino acid salvage"},{"category":"Process","description":" L-methionine salvage from methylthioadenosine"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"Hydrolase","identifier":"PF00702"}],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","kegg_map_id":null}],"gene_sequence":"ATGGTCATTGGGCAAAAGGTCCTGCTAGCTCGTATACCAAAAATGGGAGACAATTACTCGACTTACTTGCTTGATATTGAAGGGACAGTGTGCCCGATCTCGTTCGTGAAGGAGACTTTATTCCCTTATTTCACGAATAAAGTGCCGCAATTGGTTCAACAGGATACAAGGGACTCCCCGGTTTCCAACATTCTGTCGCAGTTTCACATCGACAATAAGGAGCAGTTGCAGGCGCATATTTTGGAGTTGGTGGCCAAGGATGTGAAGGATCCAATCTTGAAACAGTTGCAAGGCTACGTCTGGGCTCACGGATACGAATCTGGGCAGATTAAGGCGCCCGTTTATGCAGATGCTATTGACTTTATCAAGAGGAAGAAGCGTGTGTTTATCTACTCTAGTGGATCTGTAAAGGCACAGAAATTGCTGTTCGGGTATGTTCAGGATCCCAACGCGCCTGCGCATGATTCGTTGGATTTGAATTCTTATATAGATGGTTATTTCGACATCAACACTTCTGGAAAGAAAACCGAAACACAGTCTTACGCCAACATCTTGCGGGATATCGGTGCGAAGGCTAGCGAGGTACTGTTCTTGAGCGATAATCCATTGGAATTGGACGCAGCGGCCGGCGTTGGAATAGCTACTGGGTTAGCTTCCCGACCTGGTAATGCACCTGTCCCCGATGGGCAAAAGTACCAGGTATACAAGAATTTTGAAACTCTTTAA","protein_sequence":"MGDNYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL"},{"created_at":"2011-05-24T20:34:56.000Z","updated_at":"2011-05-27T14:56:01.000Z","name":"Methylthioribulose-1-phosphate dehydratase","uniprot_id":"P47095","uniprot_name":"MTNB_YEAST","enzyme":true,"transporter":false,"gene_name":"MDE1","num_residues":244,"molecular_weight":"27426.59961","theoretical_pi":"6.59","general_function":"Involved in metal ion binding","specific_function":"Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P)","reactions":[{"id":2329,"direction":"\u003e","locations":"Cytoplasm","altext":"S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H(2)O.","export":false,"pw_reaction_id":null,"source":null},{"id":3793,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006312","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"AY692565","genbank_protein_id":"51012581","gene_card_id":"MDE1","chromosome_location":"chromosome 10","locus":"YJR024C","synonyms":["MTRu-1-P dehydratase"],"enzyme_classes":["4.2.1.109"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" carbon-oxygen lyase activity"},{"category":"Function","description":" hydro-lyase activity"},{"category":"Process","description":" sulfur amino acid metabolic process"},{"category":"Process","description":" sulfur amino acid biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" methionine biosynthetic process"},{"category":"Process","description":" L-methionine biosynthetic process"},{"category":"Process","description":" L-methionine salvage"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular amino acid and derivative metabolic process"},{"category":"Process","description":" cellular amino acid metabolic process"}],"pfams":[{"name":"Aldolase_II","identifier":"PF00596"}],"pathways":[{"name":"Cysteine and methionine metabolism","kegg_map_id":"00270"},{"name":"Methionine metabolism and salvage","kegg_map_id":null}],"gene_sequence":"ATGTCTTCACAAGATGTTCTGATACATTCAGATGATCCGTGCCATCCAGCAAATCTCATTTGCACGCTATGCAAGCAGTTTTTTCATAATAATTGGTGCACCGGAACTGGAGGTGGGATTTCAATAAAAGATCCTAACACGAATTATTATTATCTCGCCCCATCTGGGGTGCAGAAGGAGAAGATGATACCTGAGGATTTGTTTGTCATGGACGCTCAGACATTAGAGTATTTGCGCTCTCCCAAGCTTTACAAGCCAAGCGCATGTACTCCATTGTTCTTAGCGTGCTACCAAAAGAAAAATGCAGGTGCTATAATACATACACACTCCCAAAATGCTGTGATATGCTCCTTGCTATTTGGCGATGAGTTCAGGATTGCTAACATCGAACAAATCAAAGCAATTCCAAGCGGAAAGGTGGACCCTGTGACCAAGAAACCCATGGCGCTATCGTTTTTTGATACGCTGAAGATTCCCATCATTGAAAACATGGCGCATGAGGACGAGTTGATCGATGACTTGCACAAGACTTTTAAAGATTATCCAGACACATGCGCCGTAATTGTGAGGAGACATGGCATTTTTGTTTGGGGTCCGACAATCGATAAGGCCAAAATTTTCAACGAAGCCATCGATTATTTGATGGAGCTGGCCATAAAGATGTACCAAATGGGGATTCCTCCCGACTGTGGCATTGGCGAAGAGAAGAAGCATCTGAAGATGGCCAGTCCGTGA","protein_sequence":"MSSQDVLIHSDDPCHPANLICTLCKQFFHNNWCTGTGGGISIKDPNTNYYYLAPSGVQKEKMIPEDLFVMDAQTLEYLRSPKLYKPSACTPLFLACYQKKNAGAIIHTHSQNAVICSLLFGDEFRIANIEQIKAIPSGKVDPVTKKPMALSFFDTLKIPIIENMAHEDELIDDLHKTFKDYPDTCAVIVRRHGIFVWGPTIDKAKIFNEAIDYLMELAIKMYQMGIPPDCGIGEEKKHLKMASP"}]}