{"ymdb_id":"YMDB00162","created_at":"2011-05-29T16:02:47.000Z","updated_at":"2016-09-08T18:35:07.000Z","name":"5-Thymidylic acid","cas":"365-07-1","state":"Solid","melting_point":"","description":"5-Thymidylic acid (dTMP) is a deoxyribonucleotide found in DNA. dTMP consists of a phosphate group, the sugar deoxy-ribose, and the nucleobase thymine. When found in DNA the thymine portion of dTMP pairs with the adenosine protion of dAMP.","experimental_water_solubility":"","experimental_logp_hydrophobicity":"","location":"cytoplasm","synthesis_reference":"Scarano, E.  Enzymic formation of thymidylic acid from 5-methyl-5'-deoxycytidylic acid.    Bollettino - Societa Italiana di Biologia Sperimentale  (1958),  34  945. ","chebi_id":"17013","hmdb_id":"HMDB01227","kegg_id":"C00364","pubchem_id":"9700","cs_id":"23217524","foodb_id":null,"wikipedia_link":"dTMP","biocyc_id":"TMP","iupac":"{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"thymidylate","logp":"-1.242619620666666","pka":"6.258488240760722","alogps_solubility":"6.78e+00 g/l","alogps_logp":"-1.37","alogps_logs":"-1.68","acceptor_count":"7","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"145.63000000000002","refractivity":"66.2849","polarizability":"27.459022719953495","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.240344046121354","pka_strongest_acidic":"1.2327578601680882","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2'-Deoxythymidine 5'-monophosphate","5-Methyl-dUMP","5'-dTMP","5'-Thymidylate","5'-Thymidylic acid","5'-TMP","Deoxy TMP","Deoxyribosylthymine monophosphate","Deoxythymidine 5'-monophosphate","Deoxythymidine 5'-phosphate","Deoxythymidine monophosphate","Deoxythymidylate","Deoxythymidylic acid","Deoxythymydilate","Deoxythymydilic acid","DTMP","Thymidine 5'-monophosphate","Thymidine 5'-phosphate","Thymidine 5'-phosphorate","Thymidine 5'-phosphoric acid","Thymidine 5'MP","Thymidine mononucleotide","Thymidine monophosphate","Thymidine phosphate","Thymidine-5'-monophosphorate","Thymidine-5'-monophosphoric acid","Thymidylate","Thymidylic acid"],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"One Carbon Pool by Folate I","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":18687109,"citation":"Nookaew, I., Jewett, M. C., Meechai, A., Thammarongtham, C., Laoteng, K., Cheevadhanarak, S., Nielsen, J., Bhumiratana, S. (2008). \"The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.\" BMC Syst Biol 2:71."},{"pubmed_id":6094555,"citation":"Jong, A. Y., Campbell, J. L. (1984). \"Characterization of Saccharomyces cerevisiae thymidylate kinase, the CDC8 gene product. General properties, kinetic analysis, and subcellular localization.\" J Biol Chem 259:14394-14398."},{"pubmed_id":6088527,"citation":"Jong, A. Y., Kuo, C. L., Campbell, J. L. (1984). \"The CDC8 gene of yeast encodes thymidylate kinase.\" J Biol Chem 259:11052-11059."}],"proteins":[{"created_at":"2011-05-26T17:50:40.000Z","updated_at":"2011-05-26T17:50:40.000Z","name":"Thymidylate synthase","uniprot_id":"P06785","uniprot_name":"TYSY_YEAST","enzyme":true,"transporter":false,"gene_name":"TMP1","num_residues":304,"molecular_weight":"35046.89844","theoretical_pi":"7.16","general_function":"Involved in thymidylate synthase activity","specific_function":"Required for both nuclear and mitochondrial DNA synthesis","reactions":[{"id":2013,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2487,"direction":"\u003e","locations":null,"altext":"5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP.","export":false,"pw_reaction_id":null,"source":null},{"id":14234,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006678","source":"Smpdb"},{"id":14235,"direction":"\u003e","locations":null,"altext":null,"export":true,"pw_reaction_id":"PW_R006752","source":"Smpdb"}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"J02706","genbank_protein_id":"172990","gene_card_id":"TMP1","chromosome_location":null,"locus":"YOR074C","synonyms":["TS","TSase"],"enzyme_classes":["2.1.1.45"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring one-carbon groups"},{"category":"Function","description":" methyltransferase activity"},{"category":"Function","description":" 5,10-methylenetetrahydrofolate-dependent methyltransferase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" thymidylate synthase activity"},{"category":"Process","description":" pyrimidine deoxyribonucleoside monophosphate biosynthetic process"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" dTMP biosynthetic 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"},{"category":"Process","description":" pyrimidine nucleotide metabolic process"},{"category":"Process","description":" pyrimidine nucleotide biosynthetic process"},{"category":"Process","description":" pyrimidine nucleoside monophosphate biosynthetic process"}],"pfams":[{"name":"Thymidylat_synt","identifier":"PF00303"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"One carbon pool by folate","kegg_map_id":"00670"},{"name":"One Carbon Pool by Folate I","kegg_map_id":null}],"gene_sequence":"ATGACTATGGACGGAAAAAACAAAGAAGAAGAGCAATATCTTGATCTATGCAAAAGAATCATTGATGAAGGTGAATTTAGGCCAGATAGAACAGGCACTGGTACGTTGAGTCTTTTTGCACCACCCCAGCTGCGTTTTAGTTTACGTGATGATACCTTCCCACTACTAACGACCAAGAAGGTTTTTACTAGAGGTATCATACTTGAACTATTGTGGTTTTTGGCCGGTGATACAGACGCTAACCTATTGTCTGAGCAAGGTGTTAAGATTTGGGACGGTAATGGATCTCGTGAATATTTAGATAAGATGGGGTTCAAAGATAGGAAAGTAGGAGATCTGGGGCCCGTTTACGGATTTCAATGGAGGCATTTTGGTGCTAAATACAAGACGTGCGATGACGACTATACTGGACAAGGTATTGATCAATTGAAACAGGTTATACATAAACTAAAGACAAATCCCTACGATAGAAGAATCATTATGAGTGCCTGGAACCCAGCTGATTTTGACAAAATGGCTTTGCCGCCATGCCATATTTTTTCACAGTTCTATGTCAGTTTCCCCAAAGAAGGAGAAGGATCCGGTAAGCCCCGCCTTTCATGCTTATTGTACCAACGTTCTTGTGATATGGGGTTGGGAGTACCATTTAACATTGCATCATATGCTTTGTTGACTAGAATGATTGCTAAAGTTGTCGACATGGAGCCAGGTGAGTTCATTCATACTTTGGGGGATGCACATGTTTATAAAGACCACATTGATGCCTTGAAAGAACAAATCACCAGAAATCCAAGACCATTCCCGAAACTAAAGATTAAAAGGGACGTTAAAGACATTGATGATTTCAAGTTGACAGACTTTGAAATTGAAGATTATAATCCTCATCCAAGAATTCAAATGAAAATGAGTGTATAA","protein_sequence":"MTMDGKNKEEEQYLDLCKRIIDEGEFRPDRTGTGTLSLFAPPQLRFSLRDDTFPLLTTKKVFTRGIILELLWFLAGDTDANLLSEQGVKIWDGNGSREYLDKMGFKDRKVGDLGPVYGFQWRHFGAKYKTCDDDYTGQGIDQLKQVIHKLKTNPYDRRIIMSAWNPADFDKMALPPCHIFSQFYVSFPKEGEGSGKPRLSCLLYQRSCDMGLGVPFNIASYALLTRMIAKVVDMEPGEFIHTLGDAHVYKDHIDALKEQITRNPRPFPKLKIKRDVKDIDDFKLTDFEIEDYNPHPRIQMKMSV"},{"created_at":"2011-05-26T21:15:58.000Z","updated_at":"2011-07-22T17:54:40.000Z","name":"Thymidylate kinase","uniprot_id":"P00572","uniprot_name":"KTHY_YEAST","enzyme":true,"transporter":false,"gene_name":"CDC8","num_residues":216,"molecular_weight":"24687.19922","theoretical_pi":"5.41","general_function":"Involved in thymidylate kinase activity","specific_function":"Catalyzes the conversion of dTMP to dTDP","reactions":[{"id":1474,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2607,"direction":"\u003e","locations":null,"altext":"ATP + dTMP = ADP + dTDP.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"3TMK","cellular_location":null,"genbank_gene_id":"K01783","genbank_protein_id":"171204","gene_card_id":"CDC8","chromosome_location":"chromosome 10","locus":"YJR057W","synonyms":["dTMP kinase"],"enzyme_classes":["2.7.4.9"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring phosphorus-containing groups"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"category":"Function","description":" thymidylate kinase 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":" catalytic activity"},{"category":"Function","description":" ATP binding"},{"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":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleoside diphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" pyrimidine deoxyribonucleoside diphosphate biosynthetic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" dTDP biosynthetic process"},{"category":"Process","description":" nucleoside phosphate metabolic process"},{"category":"Process","description":" nucleotide metabolic process"}],"pfams":[{"name":"Thymidylate_kin","identifier":"PF02223"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGATGGGTCGTGGCAAATTAATACTGATAGAAGGATTGGATAGGACTGGTAAAACCACGCAATGTAATATTCTTTACAAAAAATTGCAACCAAACTGTAAACTATTGAAGTTCCCCGAAAGGTCTACCCGAATCGGAGGACTCATAAACGAATATTTGACGGATGATACTTTCCAATTATCAGATCAGGCAATTCACCTCTTGTTTTCGGCAAATAGATGGGAAATAGTTGACAAGATAAAGAAAGATTTACTAGAAGGCAAGAACATTGTCATGGACAGATATGTTTATTCTGGAGTGGCATATTCTGCCGCTAAGGGGACAAATGGAATGGATTTGGATTGGTGCTTGCAACCCGATGTAGGGTTGCTGAAACCGGATTTGACATTATTTTTAAGCACTCAAGATGTCGACAATAACGCCGAAAAATCTGGATTTGGTGACGAAAGATACGAAACTGTTAAGTTTCAAGAAAAAGTGAAGCAAACTTTTATGAAGCTATTGGATAAAGAGATAAGGAAAGGCGATGAGTCAATCACGATTGTAGACGTTACTAATAAGGGCATTCAGGAAGTTGAAGCGCTTATTTGGCAAATCGTTGAGCCTGTTTTGAGTACGCATATTGATCATGATAAATTTTCGTTCTTCTAG","protein_sequence":"MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF"}]}