{"ymdb_id":"YMDB00405","created_at":"2011-05-29T18:13:32.000Z","updated_at":"2016-09-08T18:35:27.000Z","name":"Orotic acid","cas":"65-86-1","state":"Solid","melting_point":"345.5 oC","description":"Orotic acid is an 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":"1.82 mg/mL at 18 oC [YALKOWSKY,SH \u0026 HE,Y (2003)]","experimental_logp_hydrophobicity":"-0.83 [SANGSTER (1994)]","location":"Cytoplasm","synthesis_reference":"Mitchell, Herschel K.; Nyc, Joseph F. Intermediates in the synthesis of orotic acid from oxalacetic ester and urea. Journal of the American Chemical Society (1947), 69 674-7.","chebi_id":"16742","hmdb_id":"HMDB00226","kegg_id":"C00295","pubchem_id":"967","cs_id":"942","foodb_id":null,"wikipedia_link":"Orotic_acid","biocyc_id":"OROTATE","iupac":"2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid","traditional_iupac":"orotic acid","logp":"-1.227664501","pka":"8.781577888084735","alogps_solubility":"4.51e+00 g/l","alogps_logp":"-0.89","alogps_logs":"-1.54","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"1","polar_surface_area":"95.5","refractivity":"33.27460000000001","polarizability":"12.461507679606417","formal_charge":"0","physiological_charge":"-1","pka_strongest_basic":"-6.031557162374663","pka_strongest_acidic":"2.827266331449678","bioavailability":"1","number_of_rings":"1","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1,2,3,6-Tetrahydro-2,6-dioxo-4-pyrimidecarboxylic acid","2,6-dihydroxy-4-pyrimidinecarboxylic acid","2,6-Dihydroxypyrimidine-4-carboxylic acid","2,6-Dioxo-1,2,3,6-tetrahydro-pyrimidine-4-carboxylic acid","6-Carboxy-2,4-dihydroxypyrimidine","6-Carboxyuracil","6-Uracilcarboxylic acid","Animal galactose factor","Lactinium","ORO","Orodin","Oropur","Orotate","Orotic acid","Orotonin","Orotonsan","Oroturic","Orotyl","uracil-6-carboxylate","Uracil-6-carboxylic acid","Vitamin B13","Whey factor"],"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":19889834,"citation":"Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). \"Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.\" Mol Biol Cell 21:198-211."}],"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":"2011-05-27T07:14:15.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Dihydroorotate dehydrogenase","uniprot_id":"P28272","uniprot_name":"PYRD_YEAST","enzyme":true,"transporter":false,"gene_name":"URA1","num_residues":314,"molecular_weight":"34800.60156","theoretical_pi":"5.85","general_function":"Involved in catalytic activity","specific_function":"In the de novo pyrimidine biosynthesic pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate and the reduction of fumarate to succinate. Does not use oxaloacetate and NAD or NADP as electron acceptors","reactions":[{"id":1453,"direction":"\u003e","locations":"mitochondrion;mitochondrial membrane;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1454,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1554,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2803,"direction":"\u003e","locations":"Cytoplasm","altext":"(S)-dihydroorotate + O(2) = orotate + H(2)O(2).","export":false,"pw_reaction_id":null,"source":null},{"id":2804,"direction":"\u003e","locations":"Cytoplasm","altext":"(S)-dihydroorotate + a quinone = orotate + a quinol","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm","genbank_gene_id":"AJ585637","genbank_protein_id":"45719878","gene_card_id":"URA1","chromosome_location":"chromosome 11","locus":"YKL216W","synonyms":["DHOD","DHODase","DHOdehase","Dihydroorotate oxidase"],"enzyme_classes":["1.3.3.1","1.3.5.2"],"go_classes":[{"category":"Component","description":" cell part"},{"category":"Component","description":" intracellular part"},{"category":"Component","description":" cytoplasm"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" oxidoreductase activity"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-CH group of donors"},{"category":"Function","description":" dihydroorotate oxidase activity"},{"category":"Function","description":" oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor"},{"category":"Function","description":" dihydroorotate dehydrogenase activity"},{"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":" 'de novo' pyrimidine base biosynthetic process"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" oxidation reduction"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleoside monophosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" pyrimidine ribonucleoside monophosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" UMP biosynthetic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"},{"category":"Process","description":" cellular metabolic process"}],"pfams":[{"name":"DHO_dh","identifier":"PF01180"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGACAGCCAGTTTAACTACCAAGTTCTTGAACAATACCTATGAAAACCCATTTATGAATGCATCCGGTGTTCATTGCATGACTACACAAGAATTAGATGAATTAGCAAACTCTAAAGCTGGCGCATTCATTACAAAGAGTGCTACAACCTTAGAAAGAGAAGGTAACCCTGAACCACGTTACATTTCTGTCCCTCTAGGCAGTATCAACTCCATGGGTTTACCAAACGAAGGTATCGACTACTATTTGTCCTATGTATTAAACCGTCAAAAGAATTATCCTGATGCACCTGCTATTTTCTTCTCAGTTGCTGGTATGAGCATTGATGAAAATTTAAATTTGTTGAGGAAAATCCAAGATAGCGAATTCAACGGTATTACCGAGTTAAACTTGTCTTGTCCTAATGTGCCTGGGAAACCACAAGTTGCTTATGACTTTGACTTGACAAAGGAAACCTTGGAAAAGGTTTTTGCCTTTTTCAAAAAACCTCTTGGTGTCAAGTTGCCTCCTTATTTTGATTTTGCCCATTTTGATATCATGGCAAAAATATTGAACGAGTTCCCATTAGCTTATGTCAACTCTATCAATAGTATAGGAAATGGTCTTTTCATTGATGTGGAGAAGGAGAGTGTAGTAGTGAAGCCAAAGAATGGTTTCGGGGGTATTGGAGGTGAATATGTTAAGCCAACCGCGCTCGCCAATGTTCGTGCATTTTACACTCGTTTGAGACCTGAAATCAAAGTTATCGGTACAGGTGGAATTAAGTCCGGTAAGGATGCATTTGAACATCTTCTATGTGGTGCCTCTATGCTACAGATTGGTACAGAATTACAAAAAGAGGGCGTCAAGATTTTTGAACGTATCGAAAAAGAATTAAAAGACATAATGGAAGCTAAGGGTTATACATCCATAGATCAGTTCCGTGGGAAGTTGAACAGCATTTAA","protein_sequence":"MTASLTTKFLNNTYENPFMNASGVHCMTTQELDELANSKAGAFITKSATTLEREGNPEPRYISVPLGSINSMGLPNEGIDYYLSYVLNRQKNYPDAPAIFFSVAGMSIDENLNLLRKIQDSEFNGITELNLSCPNVPGKPQVAYDFDLTKETLEKVFAFFKKPLGVKLPPYFDFAHFDIMAKILNEFPLAYVNSINSIGNGLFIDVEKESVVVKPKNGFGGIGGEYVKPTALANVRAFYTRLRPEIKVIGTGGIKSGKDAFEHLLCGASMLQIGTELQKEGVKIFERIEKELKDIMEAKGYTSIDQFRGKLNSI"}]}