{"ymdb_id":"YMDB00508","created_at":"2011-05-29T18:24:50.000Z","updated_at":"2016-09-08T18:35:33.000Z","name":"2'-Deoxyuridine","cas":"951-78-0","state":"Solid","melting_point":"167 oC","description":"2'-Deoxyuridine (deoxyuridine) is a pyrimidine deoxynucleoside. It is formed by a molecule of uracil attached to a deoxyribose sugar molecule. It is considered to be an antimetabolite that is converted to deoxyuridine triphosphate during DNA synthesis.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"-1.51 [BALZARINI,JM ET AL. (1989)]","location":"extracellular;cytoplasm","synthesis_reference":"Huang, Haoqiang; Chu, Chung K. A practical synthesis of 2'-deoxyuridine from uridine. Synthetic Communications  (1990),  20(7),  1039-46.","chebi_id":"16450","hmdb_id":"HMDB00012","kegg_id":"C00526","pubchem_id":"13712","cs_id":"23630211","foodb_id":null,"wikipedia_link":"Deoxyuridine","biocyc_id":"DEOXYURIDINE","iupac":"1-[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione","traditional_iupac":"uracil deoxyriboside","logp":"-1.514604078666666","pka":"13.907903439872065","alogps_solubility":"9.06e+01 g/l","alogps_logp":"-1.49","alogps_logs":"-0.40","acceptor_count":"5","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"99.10000000000001","refractivity":"51.0549","polarizability":"20.99815409158322","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"-2.9780835884997945","pka_strongest_acidic":"9.705729612726527","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1-(2-deoxy-beta-D-ribofuranosyl)-2,4(1H,3H)-Pyrimidinedione","1-(2-Deoxy-D-erythro-pentofuranosyl)uracil","1-(2-Deoxy-delta-erythro-pentofuranosyl)uracil","2-deoxyuridine","2'-Deoxyuridine","2'-Desoxyuridine","Deoxyribose uracil","Deoxyuridine","Desoxyuridine","dU","dUrd","Uracil deoxyriboside","Uracil desoxyuridine","Uridine, 2-deoxy-","Uridine, 2'-deoxy-"],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"growth_conditions":[],"references":[{"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":"2011-05-24T20:49:32.000Z","updated_at":"2011-07-22T17:54:36.000Z","name":"Purine nucleoside phosphorylase","uniprot_id":"Q05788","uniprot_name":"PNPH_YEAST","enzyme":true,"transporter":false,"gene_name":"PNP1","num_residues":311,"molecular_weight":"33754.60156","theoretical_pi":"7.31","general_function":"Involved in purine-nucleoside phosphorylase activity","specific_function":"Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules","reactions":[{"id":1447,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1915,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1916,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1917,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1918,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1919,"direction":"\u003c\u003e","locations":"mitochondrion;cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1920,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1921,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2012,"direction":"\u003c\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2349,"direction":"\u003e","locations":null,"altext":"Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":"AY557950","genbank_protein_id":"45269792","gene_card_id":"PNP1","chromosome_location":"chromosome 12","locus":"YLR209C","synonyms":["PNP","Inosine phosphorylase"],"enzyme_classes":["2.4.2.1"],"go_classes":[{"category":"Component","description":" Not Available"},{"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":"Function","description":" purine-nucleoside phosphorylase activity"},{"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 metabolic process"}],"pfams":[{"name":"PNP_UDP_1","identifier":"PF01048"}],"pathways":[{"name":"Purine metabolism","kegg_map_id":"00230"},{"name":"Pyrimidine metabolism","kegg_map_id":"00240"},{"name":"Nicotinate and nicotinamide metabolism","kegg_map_id":"00760"}],"gene_sequence":"ATGAGTGATATCTTGAACGTAAGTCAACAACGTGAAGCAATTACCAAGGCCGCTGCGTATATTTCTGCTATTTTAGAACCACATTTCAAAAATACAACAAATTTCGAGCCTCCGAGAACTTTGATTATATGTGGTTCAGGGCTTGGTGGAATATCTACCAAGCTGTCTAGAGACAATCCACCCCCGGTAACAGTCCCATACCAAGACATCCCAGGATTCAAGAAAAGTACGGTTCCAGGTCATTCCGGTACACTAATGTTCGGATCTATGAATGGTTCACCAGTAGTATTAATGAATGGTCGTCTTCATGGATATGAAGGCAACACATTGTTTGAGACTACTTTTCCTATTAGAGTGCTTAACCACATGGGTCATGTTCGTAATTTAATTGTCACTAATGCCGCTGGTGGTATAAACGCGAAATATCAAGCCTGCGATTTGATGTGCATTTATGATCATTTAAATATCCCTGGCCTTGCTGGCCAGCACCCATTGAGAGGTCCTAACTTGGATGAAGATGGACCTCGTTTTTTAGCCTTGAGTGATGCATATGATCTGGAGTTGAGGAAGCTTTTATTTAAGAAATGGAAAGAGCTCAAGATTCAAAGGCCACTGCATGAAGGTACTTATACTTTTGTATCTGGACCCACTTTCGAAACAAGAGCAGAATCCAAAATGATAAGGATGTTGGGAGGAGATGCTGTCGGAATGAGTACTGTTCCCGAAGTCATTGTTGCAAGACATTGCGGATGGAGGGTTTTGGCCTTAAGTTTGATTACCAATACTTGCGTGGTGGATAGCCCTGCCAGTGCGTTGGACGAATCACCTGTACCCTTAGAAAAAGGCAAAGCGACTCACGCTGAAGTACTGGAGAATGGTAAAATCGCCTCTAATGACGTGCAAAACTTAATTGCTGCCGTAATGGGGGAATTATAA","protein_sequence":"MSDILNVSQQREAITKAAAYISAILEPHFKNTTNFEPPRTLIICGSGLGGISTKLSRDNPPPVTVPYQDIPGFKKSTVPGHSGTLMFGSMNGSPVVLMNGRLHGYEGNTLFETTFPIRVLNHMGHVRNLIVTNAAGGINAKYQACDLMCIYDHLNIPGLAGQHPLRGPNLDEDGPRFLALSDAYDLELRKLLFKKWKELKIQRPLHEGTYTFVSGPTFETRAESKMIRMLGGDAVGMSTVPEVIVARHCGWRVLALSLITNTCVVDSPASALDESPVPLEKGKATHAEVLENGKIASNDVQNLIAAVMGEL"},{"created_at":"2011-05-26T16:42:13.000Z","updated_at":"2011-07-22T17:54:35.000Z","name":"Cytidine deaminase","uniprot_id":"Q06549","uniprot_name":"CDD_YEAST","enzyme":true,"transporter":false,"gene_name":"CDD1","num_residues":142,"molecular_weight":"15535.90039","theoretical_pi":"7.22","general_function":"Involved in zinc ion binding","specific_function":"This enzyme scavenge exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis","reactions":[{"id":1424,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":1442,"direction":"\u003e","locations":"cytoplasm","altext":null,"export":true,"pw_reaction_id":null,"source":null},{"id":2439,"direction":"\u003e","locations":"Cytoplasmic","altext":"Cytidine + H(2)O = uridine + NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":"1R5T","cellular_location":"Cytoplasmic","genbank_gene_id":"AF080089","genbank_protein_id":"4140396","gene_card_id":"CDD1","chromosome_location":"chromosome 12","locus":"YLR245C","synonyms":["CDA","Cytidine aminohydrolase"],"enzyme_classes":["3.5.4.5"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines"},{"category":"Function","description":" cytidine deaminase activity"},{"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":"Process","description":" metabolic process"},{"category":"Process","description":" nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine nucleoside metabolic process"},{"category":"Process","description":" cellular nitrogen compound metabolic process"},{"category":"Process","description":" pyrimidine ribonucleoside metabolic process"},{"category":"Process","description":" nucleobase, nucleoside, nucleotide and nucleic acid metabolic process"},{"category":"Process","description":" cytidine metabolic process"},{"category":"Process","description":" nucleobase, nucleoside and nucleotide metabolic process"},{"category":"Process","description":" nucleoside metabolic process"}],"pfams":[{"name":"dCMP_cyt_deam_1","identifier":"PF00383"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGAAAGTAGGTGGCATAGAAGACAGACAACTGGAAGCCTTAAAAAGGGCGGCACTGAAGGCGTGTGAACTCTCCTATAGCCCCTATTCTCACTTCCGTGTCGGTTGTTCCATATTAACAAATAACGATGTTATCTTCACTGGTGCTAATGTCGAGAATGCAAGCTACAGTAATTGTATATGTGCAGAACGATCTGCTATGATACAAGTTCTAATGGCAGGCCATCGCTCAGGATGGAAATGCATGGTCATTTGTGGCGATTCTGAGGACCAGTGTGTTTCCCCTTGCGGCGTTTGCAGGCAGTTTATCAATGAATTTGTGGTCAAGGACTTTCCAATAGTCATGCTTAATTCCACAGGTTCTCGTTCTAAAGTCATGACAATGGGAGAACTGCTGCCCATGGCTTTTGGTCCATCTCATTTAAACTAG","protein_sequence":"MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHLN"}]}