{"ymdb_id":"YMDB00221","created_at":"2011-05-29T16:08:25.000Z","updated_at":"2016-09-08T18:35:12.000Z","name":"dUMP","cas":"964-26-1","state":"Solid","melting_point":null,"description":"Deoxyuridine monophosphate (dUMP) is a deoxynucleotide. It is formed by the reduction of ribonucleotides to deoxyribonucleotides by ribonucleoside diphosphate reductase [EC 1.17.4.1].","experimental_water_solubility":null,"experimental_logp_hydrophobicity":null,"location":"nucleus;cytoplasm","synthesis_reference":null,"chebi_id":"17622","hmdb_id":"HMDB01409","kegg_id":"C00365","pubchem_id":"65063","cs_id":null,"foodb_id":null,"wikipedia_link":"Deoxyuridine_monophosphate","biocyc_id":"DUMP","iupac":"{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acid","traditional_iupac":"2'-deoxyuridylic acid","logp":"-1.6381701099999995","pka":"6.258419473521287","alogps_solubility":"7.97e+00 g/l","alogps_logp":"-1.42","alogps_logs":"-1.59","acceptor_count":"7","donor_count":"4","rotatable_bond_count":"4","polar_surface_area":"145.63","refractivity":"61.927800000000005","polarizability":"25.855873865751356","formal_charge":"0","physiological_charge":"-2","pka_strongest_basic":"-3.240343942911336","pka_strongest_acidic":"1.232757608087275","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["2'-Deoxy-5'-uridylate","2'-Deoxy-5'-uridylic acid","2'-Deoxyuridine 5'-monophosphate","2'-Deoxyuridine 5'-phosphate","2'-Deoxyuridylate","2'-Deoxyuridylic acid","Deoxy-UMP","Deoxyuridine 5'-monophosphate","Deoxyuridine 5'-phosphate","Deoxyuridine monophosphate","Deoxyuridylate","Deoxyuridylic 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":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":"2011-05-26T16:39:20.000Z","updated_at":"2011-05-27T15:01:00.000Z","name":"Uridylate kinase","uniprot_id":"P15700","uniprot_name":"UMPK_YEAST","enzyme":true,"transporter":false,"gene_name":"URA6","num_residues":204,"molecular_weight":"22933.0","theoretical_pi":"6.53","general_function":"Involved in ATP binding","specific_function":"Furnishes the cell with pyrimidines. Accepts UMP, and dUMP as phosphate acceptors with high activity; to a lesser extent, it can also use IMP, GMP, dGMP, 5-iodo-dUMP, XMP, and dTMP as substrates. ATP and dATP are the best phosphate donors; can use GTP, dGTP, dCTP, and dTTP to some degree (30-50%)","reactions":[{"id":2033,"direction":"\u003c\u003e","locations":"cytoplasm;nucleus","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2039,"direction":"\u003c\u003e","locations":"cytoplasm;nucleus","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2436,"direction":"\u003e","locations":"Cytoplasm. Nucleus.","altext":"ATP + UMP = ADP + UDP.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1UKZ","cellular_location":"Cytoplasm. Nucleus.","genbank_gene_id":"AY558074","genbank_protein_id":"45270038","gene_card_id":"URA6","chromosome_location":"chromosome 11","locus":"YKL024C","synonyms":["UK","Uridine monophosphate kinase","UMP kinase"],"enzyme_classes":["2.7.4.-"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" nucleobase, nucleoside, nucleotide kinase activity"},{"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":" nucleotide kinase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" phosphotransferase activity, phosphate group as acceptor"},{"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"}],"pfams":[{"name":"ADK","identifier":"PF00406"}],"pathways":[],"gene_sequence":"ATGACAGCTGCCACTACATCACAGCCAGCTTTCTCGCCTGACCAAGTTTCCGTGATCTTCGTTCTAGGAGGACCCGGTGCAGGCAAGGGTACTCAGTGTGAAAAACTAGTTAAGGACTATTCATTTGTCCATTTGTCAGCCGGAGACCTTCTACGTGCTGAGCAGGGCAGAGCAGGTTCCCAATATGGGGAATTGATCAAGAACTGCATCAAAGAGGGCCAGATTGTCCCTCAAGAGATTACTTTGGCGCTTTTACGCAACGCTATTTCCGATAACGTCAAGGCGAACAAGCATAAGTTCTTAATTGACGGATTTCCTAGGAAGATGGATCAAGCCATTTCCTTTGAAAGAGACATCGTTGAAAGCAAATTCATCCTGTTCTTTGACTGCCCTGAAGATATCATGTTAGAGAGACTATTGGAGCGTGGCAAGACCAGTGGTAGAAGCGATGACAACATTGAGTCCATTAAGAAGAGATTTAACACTTTCAAGGAGACTAGTATGCCCGTCATCGAGTACTTTGAAACCAAATCGAAAGTCGTCCGTGTTCGTTGCGACAGATCCGTCGAAGATGTGTACAAAGACGTCCAAGACGCTATCCGTGATAGCTTATAG","protein_sequence":"MTAATTSQPAFSPDQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLRAEQGRAGSQYGELIKNCIKEGQIVPQEITLALLRNAISDNVKANKHKFLIDGFPRKMDQAISFERDIVESKFILFFDCPEDIMLERLLERGKTSGRSDDNIESIKKRFNTFKETSMPVIEYFETKSKVVRVRCDRSVEDVYKDVQDAIRDSL"},{"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":"2011-05-26T18:17:59.000Z","updated_at":"2011-07-22T17:54:35.000Z","name":"Deoxycytidylate deaminase","uniprot_id":"P06773","uniprot_name":"DCTD_YEAST","enzyme":true,"transporter":false,"gene_name":"DCD1","num_residues":312,"molecular_weight":"35645.69922","theoretical_pi":"7.95","general_function":"Involved in zinc ion binding","specific_function":"Supplies the nucleotide substrate for thymidylate synthetase","reactions":[{"id":1438,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1439,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2522,"direction":"\u003e","locations":"Cytoplasmic","altext":"dCMP + H(2)O = dUMP + NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"M13010","genbank_protein_id":"171384","gene_card_id":"DCD1","chromosome_location":"chromosome 8","locus":"YHR144C","synonyms":["dCMP deaminase"],"enzyme_classes":["3.5.4.12"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" binding"},{"category":"Function","description":" ion binding"},{"category":"Function","description":" cation binding"},{"category":"Function","description":" metal ion binding"},{"category":"Function","description":" transition metal ion binding"},{"category":"Function","description":" zinc ion binding"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" Not Available"}],"pfams":[{"name":"dCMP_cyt_deam_1","identifier":"PF00383"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGTTAATTGGTGTAAGTGGTACGAAATTTTGCGGATGCGAAGATGTTATTAACATGTTGGTTGATCATTTTCATTTTGAATTACTCAATCACCTAGATAATCCAGAGGAGATATTAGATTATGCTACGAAAAATTACACAAAAAATTCAGTTATATTCCTAGAAAAATTATCATTACTGGAGAAACTGGAAAAGAGACCATTTTTTGTTCATCTTTCTATCGACGCTCCTGCTACTACAAGGGTAGCATTATACAGGAAAACGACTCAAGCAGAAAGCTTATCATTAGAACAAATAATACAAGCCATTGATCAACATGACTTTCAGCCTGAAGGCATCAAATTAAGGGAGAAATCCCATTTGAGATTTAAAATAGTTAATGAGGACCGCAGAGGAAGGAGACAGAGCTTGATTAATAACATTACCACACAATTAAAGATTCTCGATGACAAAGAGAAACAAATGGCTCCATTAATGAGGCCTAGTTGGGATAGCTATTTTATGAAGTTAGCCACACTAGCAGCATCTCGTTCCAATTGCATGAAACGTAGAGTTGGTTGCGTGATTGTGAGAGAATGCAGAGTGATTGCTACTGGCTATAATGGGACTCCTCGACATTTAACAAATTGTTTCAATGGCGGTTGCCCACGTTGCAATGACGGTGATTCTAGAAATCTGCACACTTGCTTATGCTTACATGCAGAAGAGAATGCACTACTGGAAGCTGGCAGGGATCGTGTAGGTCAAAATGCGACCTTATACTGTGATACTTGCCCTTGCTTAACATGTTCTGTAAAGATTGTTCAAACAGGCATCAGTGAAGTAGTTTATAGCCAAAGTTATAGAATGGACGAGGAAAGTTTCAAGGTCTTGAAGAATGCGGGAATAACCGTCCGGCAATTCAGCTTTACGGAAGAACCAAGAATTGTGATGATTTAA","protein_sequence":"MLIGVSGTKFCGCEDVINMLVDHFHFELLNHLDNPEEILDYATKNYTKNSVIFLEKLSLLEKLEKRPFFVHLSIDAPVTTRVALYRKTTQAESLSLEQIIQAIDQHDFQPEGIKLREKSHLRFKIVNEDRRGRRQSLINNITTQLKILDDKEKQMAPLMRPSWDSYFMKLATLAASRSNCMKRRVGCVIVRECRVIATGYNGTPRHLTNCFNGGCPRCNDGDSRNLHTCLCLHAEENALLEAGRDRVGQNATLYCDTCPCLTCSVKIVQTGISEVVYSQSYRMDEESFKVLKNAGITVRQFSFTEEPRIVMI"},{"created_at":"2011-05-27T03:50:41.000Z","updated_at":"2011-07-22T17:54:40.000Z","name":"Deoxyuridine 5'-triphosphate nucleotidohydrolase","uniprot_id":"P33317","uniprot_name":"DUT_YEAST","enzyme":true,"transporter":false,"gene_name":"DUT1","num_residues":147,"molecular_weight":"15307.2002","theoretical_pi":"7.52","general_function":"Involved in hydrolase activity","specific_function":"This enzyme is involved in nucleotide metabolism:it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA","reactions":[{"id":1475,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2747,"direction":"\u003e","locations":"Cytoplasmic","altext":"dUTP + H(2)O = dUMP + diphosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasmic","genbank_gene_id":"AY693064","genbank_protein_id":"51013579","gene_card_id":"DUT1","chromosome_location":"chromosome 2","locus":"YBR252W","synonyms":["dUTPase","dUTP pyrophosphatase"],"enzyme_classes":["3.6.1.23"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydrolase activity"},{"category":"Function","description":" hydrolase activity, acting on acid anhydrides"},{"category":"Function","description":" hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides"},{"category":"Function","description":" pyrophosphatase activity"},{"category":"Function","description":" nucleoside-triphosphate diphosphatase activity"},{"category":"Function","description":" dUTP diphosphatase activity"},{"category":"Function","description":" catalytic activity"},{"category":"Process","description":" metabolic process"},{"category":"Process","description":" pyrimidine deoxyribonucleoside triphosphate metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" dUTP 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 nucleoside triphosphate metabolic process"}],"pfams":[{"name":"dUTPase","identifier":"PF00692"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGACTGCTACTAGCGACAAAGTACTAAAGATTCAATTGCGCTCAGCAAGCGCTACTGTACCTACCAAAGGTTCTGCCACTGCCGCGGGATACGACATTTATGCATCTCAGGATATTACCATTCCGGCTATGGGTCAAGGTATGGTTTCCACCGACATATCGTTCACCGTACCTGTTGGTACCTACGGTCGTATTGCGCCAAGGTCAGGCCTGGCAGTGAAAAACGGTATCCAAACCGGTGCTGGTGTTGTCGACAGAGATTACACCGGTGAAGTTAAAGTAGTTTTATTCAATCATTCACAGAGGGATTTCGCGATCAAAAAAGGTGATCGCGTAGCCCAATTGATTCTGGAAAAAATTGTCGATGATGCCCAGATCGTTGTTGTAGACTCTCTGGAAGAAAGTGCAAGAGGGGCCGGTGGCTTTGGTAGCACTGGTAACTAA","protein_sequence":"MTATSDKVLKIQLRSASATVPTKGSATAAGYDIYASQDITIPAMGQGMVSTDISFTVPVGTYGRIAPRSGLAVKNGIQTGAGVVDRDYTGEVKVVLFNHSQRDFAIKKGDRVAQLILEKIVDDAQIVVVDSLEESARGAGGFGSTGN"}]}