{"ymdb_id":"YMDB00504","created_at":"2011-05-29T18:24:29.000Z","updated_at":"2016-09-08T18:35:33.000Z","name":"2'-Deoxycytidine","cas":"951-77-9","state":"Solid","melting_point":"207-210 oC","description":"2'-Deoxycytidine (deoxycytidine) is a pyrimidine deoxyribonucleoside. It is formed by a molecule of cytosine attached to a deoxyribose sugar molecule. Deoxycytidine is the DNA deoxynucleoside C.","experimental_water_solubility":null,"experimental_logp_hydrophobicity":"-1.77 [HANSCH,C ET AL. (1995)]","location":"extracellular;cytoplasm","synthesis_reference":" Fox, Jack F.; Yung, Naishun; Wempen, Iris; Hoffer, Max. Pyrimidine nucleosides. XII. Direct synthesis of 2'-deoxycytidine and its a-anomer. Journal of the American Chemical Society  (1961),  83  4066-50. ","chebi_id":"15698","hmdb_id":"HMDB00014","kegg_id":"C00881","pubchem_id":"13711","cs_id":"23076092","foodb_id":null,"wikipedia_link":"Deoxycytidine","biocyc_id":"DEOXYCYTIDINE","iupac":"4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one","traditional_iupac":"2'-deoxycytidine","logp":"-1.8968792213333328","pka":"14.78753514288664","alogps_solubility":"1.59e+01 g/l","alogps_logp":"-1.93","alogps_logs":"-1.16","acceptor_count":"6","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"108.38","refractivity":"53.0341","polarizability":"21.64578911898849","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"0.3081753362314522","pka_strongest_acidic":"13.894899521324458","bioavailability":"1","number_of_rings":"2","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["1-(2-Deoxy-b-D-ribofuranosyl)cytosine","1-(2-deoxy-beta-D-erythro-pentofuranosyl)-Cytosine","1-(2-Deoxy-beta-D-ribofuranosyl)cytosine","1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-Cytosine","1-(2-Deoxy-beta-delta-ribofuranosyl)cytosine","2-deoxy-Cytidine","2-deoxycytidine","2'-Deoxycytidine","4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2(1H)-one","Cytidine, 2'-deoxy-","Cytosine deoxyribonucleoside","Cytosine deoxyriboside","Cytosine, 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-","dC","dCyd","DCZ","deoxy-Cytidine","Deoxycytidine","Deoxyribose cytidine","Desoxycytidine"],"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."},{"pubmed_id":12111094,"citation":"Kurtz, J. E., Exinger, F., Erbs, P., Jund, R. (2002). \"The URH1 uridine ribohydrolase of Saccharomyces cerevisiae.\" Curr Genet 41:132-141."}],"proteins":[{"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":" 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":" 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":"Process","description":" nucleoside metabolic process"},{"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"}],"pfams":[{"name":"dCMP_cyt_deam_1","identifier":"PF00383"}],"pathways":[{"name":"Pyrimidine metabolism","kegg_map_id":"00240"}],"gene_sequence":"ATGAAAGTAGGTGGCATAGAAGACAGACAACTGGAAGCCTTAAAAAGGGCGGCACTGAAGGCGTGTGAACTCTCCTATAGCCCCTATTCTCACTTCCGTGTCGGTTGTTCCATATTAACAAATAACGATGTTATCTTCACTGGTGCTAATGTCGAGAATGCAAGCTACAGTAATTGTATATGTGCAGAACGATCTGCTATGATACAAGTTCTAATGGCAGGCCATCGCTCAGGATGGAAATGCATGGTCATTTGTGGCGATTCTGAGGACCAGTGTGTTTCCCCTTGCGGCGTTTGCAGGCAGTTTATCAATGAATTTGTGGTCAAGGACTTTCCAATAGTCATGCTTAATTCCACAGGTTCTCGTTCTAAAGTCATGACAATGGGAGAACTGCTGCCCATGGCTTTTGGTCCATCTCATTTAAACTAG","protein_sequence":"MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSEDQCVSPCGVCRQFINEFVVKDFPIVMLNSTGSRSKVMTMGELLPMAFGPSHLN"}]}