{"ymdb_id":"YMDB00025","created_at":"2011-05-29T15:49:35.000Z","updated_at":"2016-09-08T18:34:55.000Z","name":"Orotidylic acid","cas":"2149-82-8","state":"Solid","melting_point":"","description":"Orotidylic acid (orotidine 5'-monophosphate) is the last intermediate in the uridine-5'-phosphate biosynthesis pathway. Uridine-5'-phosphate (UMP) is a pyrimidine used for the de novo biosynthesis of pyrimidine nucleotides. [Biocyc PWY-5686]","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Ueda, Tohru; Yamamoto, Miyako; Yamane, Akira; Imazawa, Masaoki; Inoue, Hideo.  Nucleosides and nucleotides.  XXIII.  Conversion of uridine nucleotides to the 6-cyano derivatives:  synthesis of orotidylic acid.    Journal of Carbohydrates, Nucleosides, Nuc","chebi_id":"15842","hmdb_id":"HMDB00218","kegg_id":"C01103","pubchem_id":"160617","cs_id":"141140","foodb_id":null,"wikipedia_link":"Orotidine_5'-monophosphate","biocyc_id":"OROTIDINE-5-PHOSPHATE","iupac":"3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid","traditional_iupac":"6-carboxy-5'-uridylic acid","logp":"-2.911181674","pka":"2.8807694070808423","alogps_solubility":"8.61e+00 g/l","alogps_logp":"-1.67","alogps_logs":"-1.63","acceptor_count":"10","donor_count":"6","rotatable_bond_count":"5","polar_surface_area":"203.16","refractivity":"70.7438","polarizability":"29.646566664527832","formal_charge":"0","physiological_charge":"-3","pka_strongest_basic":"-3.6645573647317757","pka_strongest_acidic":"1.21301296157929","bioavailability":"0","number_of_rings":"2","rule_of_five":"0","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylate","1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylic acid","1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylate","1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylic acid","2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid","2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid","5-(Dihydrogen phosphate)orotidine","5'-(dihydrogen phosphate) 6-carboxy-uridine","5'-(dihydrogen phosphate) Orotidine","5'-OMP","5'-phosphate Orotidine","6-carboxy-5'-uridylate","6-carboxy-5'-uridylic acid","Ometoprim","OMP","Omp (nucleotide)","orotidine 5'-(dihydrogen phosphate)","Orotidine 5'-(dihydrogen phosphoric acid)","Orotidine 5'-monophosphate","Orotidine 5'-phosphate","Orotidine monophosphate","orotidine-5'-phosphate","Orotidylate","Orotidylic acid"],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"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":218950,"citation":"Victor, J., Greenberg, L. B., Sloan, D. L. (1979). \"Studies of the kinetic mechanism of orotate phosphoribosyltransferase from yeast.\" J Biol Chem 254:2647-2655."},{"pubmed_id":18020427,"citation":"Gonzalez-Segura, L., Witte, J. F., McClard, R. W., Hurley, T. D. (2007). \"Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase.\" Biochemistry 46:14075-14086."}],"proteins":[{"created_at":"2011-05-24T20:35:26.000Z","updated_at":"2011-05-27T14:56:01.000Z","name":"Orotate phosphoribosyltransferase 1","uniprot_id":"P13298","uniprot_name":"PYRE_YEAST","enzyme":true,"transporter":false,"gene_name":"URA5","num_residues":226,"molecular_weight":"24664.19922","theoretical_pi":"5.85","general_function":"Involved in orotate phosphoribosyltransferase activity","specific_function":"Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)","reactions":[{"id":1808,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2330,"direction":"\u003e","locations":"","altext":"Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY693160","genbank_protein_id":"51013771","gene_card_id":"URA5","chromosome_location":"chromosome 13","locus":"YML106W","synonyms":["OPRT 1","OPRTase 1"],"enzyme_classes":["2.4.2.10"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" orotate phosphoribosyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" nucleoside metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"}],"pfams":[{"name":"Pribosyltran","identifier":"PF00156"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGCCTATTATGTTGGAAGACTACCAAAAGAACTTTCTAGAGTTGGCCATCGAATGCCAGGCTCTAAGATTTGGTTCATTCAAGTTGAAATCAGGTAGAGAATCGCCATATTTCTTTAATTTGGGATTGTTCAATACTGGTAAATTGCTTTCCAATTTGGCTACTGCGTATGCAATTGCCATCATACAATCTGATTTGAAATTTGATGTGATTTTCGGTCCTGCCTACAAAGGTATCCCACTTGCTGCTATTGTTTGTGTGAAATTGGCGGAGATTGGTGGCTCTAAATTTCAAAACATTCAGTACGCTTTTAACAGAAAGGAAGCCAAAGATCATGGTGAAGGTGGTATCATTGTCGGCTCTGCCCTAGAGAACAAGAGAATATTAATCATCGACGACGTCATGACTGCTGGTACTGCCATTAACGAGGCCTTTGAGATCATCAGTAACGCCAAGGGTCAGGTAGTTGGCTCCATAATTGCTCTTGATAGACAGGAAGTTGTGAGTACTGACGATAAAGAAGGACTCAGCGCCACTCAAACTGTTAGCAAAAAATACGGTATCCCAGTCTTGAGCATTGTCTCCTTAATTCACATAATTACCTATTTGGAAGGCAGAATAACAGCAGAAGAGAAAAGCAAGATCGAACAATACCTTCAAACCTACGGTGCCTCCGCTTAA","protein_sequence":"MPIMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGASA"},{"created_at":"2011-05-24T20:35:55.000Z","updated_at":"2011-05-27T14:56:01.000Z","name":"Orotate phosphoribosyltransferase 2","uniprot_id":"P30402","uniprot_name":"PYRX_YEAST","enzyme":true,"transporter":false,"gene_name":"URA10","num_residues":227,"molecular_weight":"24810.30078","theoretical_pi":"8.76","general_function":"Involved in orotate phosphoribosyltransferase activity","specific_function":"Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)","reactions":[{"id":1808,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2330,"direction":"\u003e","locations":"","altext":"Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.","export":false,"pw_reaction_id":null,"source":null},{"id":14251,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006735","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY557976","genbank_protein_id":"45269844","gene_card_id":"URA10","chromosome_location":"chromosome 13","locus":"YMR271C","synonyms":["OPRT 2","OPRTase 2"],"enzyme_classes":["2.4.2.10"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" orotate phosphoribosyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring glycosyl groups"},{"category":"Function","description":" transferase activity, transferring pentosyl groups"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" nucleoside metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"}],"pfams":[{"name":"Pribosyltran","identifier":"PF00156"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGTCTGCATCTACTACAAGTTTAGAGGAATATCAAAAAACTTTCCTTGAACTGGGATTAGAATGCAAAGCACTAAGATTTGGGTCATTCAAGCTGAATTCAGGCAGGCAGTCGCCATATTTTTTCAATCTTAGTTTGTTCAATTCTGGAAAGCTGTTGGCAAACCTTGCCACCGCGTATGCAACTGCTATCATTCAATCGGAGCTTAAATTCGATGTTATTTTCGGACCTGCTTACAAAGGGATCCCTTTGGCTGCTATTGTATGCGTTAAACTAGCAGAAATCGGGGGCACTAAATTTCAAGGTATTCAATATGCTTTTAATAGAAAGAAAGTTAAAGACCACGGCGAAGGTGGTATTATTGTTGGAGCATCGCTTGAAGACAAGAGGGTGTTGATTATCGACGATGTCATGACTGCAGGAACTGCAATCAATGAAGCATTTGAGATAATCAGTATTGCTCAAGGTAGGGTAGTGGGTTGTATTGTTGCTTTAGATAGGCAAGAAGTGATTCATGAATCTGATCCGGAAAGAACAAGTGCTACCCAATCTGTTTCAAAGAGATACAACGTTCCTGTGCTAAGTATTGTATCACTGACTCAAGTGGTACAATTTATGGGAAATAGACTATCACCAGAGCAAAAATCAGCGATTGAAAACTACCGTAAGGCCTATGGTATATGA","protein_sequence":"MSASTTSLEEYQKTFLELGLECKALRFGSFKLNSGRQSPYFFNLSLFNSGKLLANLATAYATAIIQSELKFDVIFGPAYKGIPLAAIVCVKLAEIGGTKFQGIQYAFNRKKVKDHGEGGIIVGASLEDKRVLIIDDVMTAGTAINEAFEIISIAQGRVVGCIVALDRQEVIHESDPERTSATQSVSKRYNVPVLSIVSLTQVVQFMGNRLSPEQKSAIENYRKAYGI"},{"created_at":"2011-05-24T20:36:50.000Z","updated_at":"2011-05-27T14:56:01.000Z","name":"Orotidine 5'-phosphate decarboxylase","uniprot_id":"P03962","uniprot_name":"PYRF_YEAST","enzyme":true,"transporter":false,"gene_name":"URA3","num_residues":267,"molecular_weight":"29239.30078","theoretical_pi":"7.45","general_function":"Involved in catalytic activity","specific_function":"Orotidine 5'-phosphate = UMP + CO(2)","reactions":[{"id":1809,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2331,"direction":"\u003e","locations":null,"altext":"Orotidine 5'-phosphate = UMP + CO(2).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1DQX","cellular_location":null,"genbank_gene_id":"K02206","genbank_protein_id":"172060","gene_card_id":"URA3","chromosome_location":"chromosome 5","locus":"YEL021W","synonyms":["OMP decarboxylase","OMPDCase","OMPdecase","Uridine 5'-monophosphate synthase","UMP synthase"],"enzyme_classes":["4.1.1.23"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" orotidine-5'-phosphate decarboxylase activity"},{"category":"Function","description":" lyase activity"},{"category":"Function","description":" carbon-carbon lyase activity"},{"category":"Function","description":" carboxy-lyase activity"},{"category":"Process","description":" cellular metabolic process"},{"category":"Process","description":" cellular aromatic compound metabolic process"},{"category":"Process","description":" nucleobase metabolic process"},{"category":"Process","description":" pyrimidine base metabolic process"},{"category":"Process","description":" pyrimidine base biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" 'de novo' pyrimidine base biosynthetic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" pyrimidine nucleoside monophosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" pyrimidine ribonucleoside monophosphate biosynthetic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" UMP biosynthetic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" 'de novo' UMP biosynthetic process"}],"pfams":[{"name":"OMPdecase","identifier":"PF00215"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGTCGAAAGCTACATATAAGGAACGTGCTGCTACTCATCCTAGTCCTGTTGCTGCCAAGCTATTTAATATCATGCACGAAAAGCAAACAAACTTGTGTGCTTCATTGGATGTTCGTACCACCAAGGAATTACTGGAGTTAGTTGAAGCATTAGGTCCCAAAATTTGTTTACTAAAAACACATGTGGATATCTTGACTGATTTTTCCATGGAGGGCACAGTTAAGCCGCTAAAGGCATTATCCGCCAAGTACAATTTTTTACTCTTCGAAGACAGAAAATTTGCTGACATTGGTAATACAGTCAAATTGCAGTACTCTGCGGGTGTATACAGAATAGCAGAATGGGCAGACATTACGAATGCACACGGTGTGGTGGGCCCAGGTATTGTTAGCGGTTTGAAGCAGGCGGCAGAAGAAGTAACAAAGGAACCTAGAGGCCTTTTGATGTTAGCAGAATTGTCATGCAAGGGCTCCCTATCTACTGGAGAATATACTAAGGGTACTGTTGACATTGCGAAGAGCGACAAAGATTTTGTTATCGGCTTTATTGCTCAAAGAGACATGGGTGGAAGAGATGAAGGTTACGATTGGTTGATTATGACACCCGGTGTGGGTTTAGATGACAAGGGAGACGCATTGGGTCAACAGTATAGAACCGTGGATGATGTGGTCTCTACAGGATCTGACATTATTATTGTTGGAAGAGGACTATTTGCAAAGGGAAGGGATGCTAAGGTAGAGGGTGAACGTTACAGAAAAGCAGGCTGGGAAGCATATTTGAGAAGATGCGGCCAGCAAAACTAA","protein_sequence":"MSKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEALGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNTVKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLMLAELSCKGSLATGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIMTPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGERYRKAGWEAYLRRCGQQN"}]}