2.0 2012-05-31 09:55:17 -0600 2015-09-13 12:56:05 -0600 ECMDB00014 M2MDB000003 Deoxycytidine Deoxycytidine is one of the principal nucleosides of DNA composed of cytosine and deoxyribose. A nucleoside consists of only a pentose sugar linked to a purine or pyrimidine base, without a phosphate group. When N1 is linked to the C1 of deoxyribose, deoxynucleosides and nucleotides are formed from cytosine and deoxyribose; deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP), deoxycytidine triphosphate (dCTP). CTP is the source of the cytidine in RNA (ribonucleic acid) and deoxycytidine triphosphate (dCTP) is the source of the deoxycytidine in DNA (deoxyribonucleic acid). 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-cytosine 1-(2-Deoxy-b-D-ribofuranosyl)cytosine 1-(2-Deoxy-b-delta-erythro-pentofuranosyl)-cytosine 1-(2-Deoxy-b-delta-ribofuranosyl)cytosine 1-(2-Deoxy-b-δ-erythro-pentofuranosyl)-cytosine 1-(2-Deoxy-b-δ-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 1-(2-Deoxy-β-D-erythro-pentofuranosyl)-cytosine 1-(2-Deoxy-β-D-ribofuranosyl)cytosine 1-(2-Deoxy-β-δ-erythro-pentofuranosyl)-cytosine 1-(2-Deoxy-β-δ-ribofuranosyl)cytosine 2'-Deoxycytidine 2-Deoxy-Cytidine 4-Amino-1-(2-deoxy-b-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-amino-1-(2-Deoxy-b-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-amino-1-(2-Deoxy-b-δ-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-Amino-1-(2-deoxy-beta-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-Amino-1-(2-deoxy-beta-delta-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-amino-1-(2-Deoxy-β-D-erythro-pentofuranosyl)-2(1H)-pyrimidinone 4-amino-1-(2-Deoxy-β-δ-erythro-pentofuranosyl)-2(1H)-pyrimidinone Cytosine deoxyribonucleoside Cytosine deoxyriboside D-Cytidine DCyt Deoxy-Cytidine Deoxyribose cytidine Desoxycytidine C9H13N3O4 227.2172 227.090605919 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one 2'-deoxycytidine 951-77-9 NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1 InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1 CKTSBUTUHBMZGZ-SHYZEUOFSA-N Solid Cytosol Extra-organism Periplasm logp -1.93 ALOGPS logs -1.16 ALOGPS solubility 1.59e+01 g/l ALOGPS melting_point 207-210 oC logp -1.9 ChemAxon pka_strongest_acidic 13.89 ChemAxon pka_strongest_basic 0.31 ChemAxon iupac 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one ChemAxon average_mass 227.2172 ChemAxon mono_mass 227.090605919 ChemAxon smiles NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](CO)O1 ChemAxon formula C9H13N3O4 ChemAxon inchi InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m0/s1 ChemAxon inchikey CKTSBUTUHBMZGZ-SHYZEUOFSA-N ChemAxon polar_surface_area 108.38 ChemAxon refractivity 53.03 ChemAxon polarizability 21.65 ChemAxon rotatable_bond_count 2 ChemAxon acceptor_count 6 ChemAxon donor_count 3 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Pyrimidine metabolism The metabolism of pyrimidines begins with L-glutamine interacting with water molecule and a hydrogen carbonate through an ATP driven carbamoyl phosphate synthetase resulting in a hydrogen ion, an ADP, a phosphate, an L-glutamic acid and a carbamoyl phosphate. The latter compound interacts with an L-aspartic acid through a aspartate transcarbamylase resulting in a phosphate, a hydrogen ion and a N-carbamoyl-L-aspartate. The latter compound interacts with a hydrogen ion through a dihydroorotase resulting in the release of a water molecule and a 4,5-dihydroorotic acid. This compound interacts with an ubiquinone-1 through a dihydroorotate dehydrogenase, type 2 resulting in a release of an ubiquinol-1 and an orotic acid. The orotic acid then interacts with a phosphoribosyl pyrophosphate through a orotate phosphoribosyltransferase resulting in a pyrophosphate and an orotidylic acid. The latter compound then interacts with a hydrogen ion through an orotidine-5 '-phosphate decarboxylase, resulting in an release of carbon dioxide and an Uridine 5' monophosphate. The Uridine 5' monophosphate process to get phosphorylated by an ATP driven UMP kinase resulting in the release of an ADP and an Uridine 5--diphosphate. Uridine 5-diphosphate can be metabolized in multiple ways in order to produce a Deoxyuridine triphosphate. 1.-Uridine 5-diphosphate interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in the release of a water molecule and an oxidized thioredoxin and an dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 2.-Uridine 5-diphosphate interacts with a reduced NrdH glutaredoxin-like protein through a Ribonucleoside-diphosphate reductase 1 resulting in a release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 3.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate. The latter compound interacts with a reduced flavodoxin through ribonucleoside-triphosphate reductase resulting in the release of an oxidized flavodoxin, a water molecule and a Deoxyuridine triphosphate 4.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in the release of a water molecule, an oxidized flavodoxin and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 5.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP then interacts with a reduced NrdH glutaredoxin-like protein through a ribonucleoside-diphosphate reductase 2 resulting in the release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 6.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. The deoxyuridine triphosphate then interacts with a water molecule through a nucleoside triphosphate pyrophosphohydrolase resulting in a release of a hydrogen ion, a phosphate and a dUMP. The dUMP then interacts with a methenyltetrahydrofolate through a thymidylate synthase resulting in a dihydrofolic acid and a 5-thymidylic acid. Then 5-thymidylic acid is then phosphorylated through a nucleoside diphosphate kinase resulting in the release of an ADP and thymidine 5'-triphosphate. PW000942 ec00240 Metabolic Drug metabolism - other enzymes ec00983 Metabolic pathways eco01100 pyrimidine deoxyribonucleosides degradation The degradation of deoxycytidine starts with deoxycytidine being introduced into the cytosol through either a nupG or nupC symporter. Once inside, it can can be degrade through water,a hydrogen ion and a deoxycytidien deaminsa resultin in the release of a ammonium and a a deoxyuridine. The deoxyuridine is then degraded through a uracil phosphorylase resulting in the release of a deoxyribose 1-phosphate and a uracil. The degradation of thymidine starts with thymidine being introduced into the cytosol through either a nupG or nupC symporter. Thymidine is then degrades through a phosphorylase resulting in the release of a thymine and a deoxyribose 1-phosphate. PW002063 Metabolic salvage pathways of pyrimidine deoxyribonucleotides The pathway begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter. Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP. Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP PW002061 Metabolic salvage pathways of pyrimidine deoxyribonucleotides PWY0-181 pyrimidine deoxyribonucleosides degradation PWY0-1298 Specdb::CMs 3171 Specdb::CMs 37243 Specdb::CMs 137113 Specdb::CMs 144847 Specdb::CMs 1046911 Specdb::CMs 1046912 Specdb::CMs 1046914 Specdb::CMs 1046916 Specdb::CMs 1046918 Specdb::CMs 1046920 Specdb::CMs 1046921 Specdb::CMs 1046923 Specdb::CMs 1046925 Specdb::CMs 1046927 Specdb::CMs 1046929 Specdb::CMs 1046931 Specdb::CMs 1046933 Specdb::NmrOneD 1029 Specdb::NmrOneD 1119 Specdb::NmrOneD 166476 Specdb::MsMs 22 Specdb::MsMs 23 Specdb::MsMs 24 Specdb::MsMs 2533 Specdb::MsMs 2534 Specdb::MsMs 2535 Specdb::MsMs 2536 Specdb::MsMs 2537 Specdb::MsMs 2538 Specdb::MsMs 2539 Specdb::MsMs 2540 Specdb::MsMs 2541 Specdb::MsMs 2542 Specdb::MsMs 2543 Specdb::MsMs 2544 Specdb::MsMs 2545 Specdb::MsMs 2546 Specdb::MsMs 179610 Specdb::MsMs 179611 Specdb::MsMs 179612 Specdb::MsMs 181941 Specdb::MsMs 181942 Specdb::MsMs 181943 Specdb::MsMs 437549 Specdb::MsMs 437550 Specdb::NmrTwoD 922 HMDB00014 13711 13117 C00881 DEOXYCYTIDINE DCZ Deoxycytidine Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. 21097882 Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. 22080510 van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. 17765195 Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. 18331064 van den Bosch J, Lubbert M, Verhoef G, Wijermans PW: The effects of 5-aza-2'-deoxycytidine (Decitabine) on the platelet count in patients with intermediate and high-risk myelodysplastic syndromes. Leuk Res. 2004 Aug;28(8):785-90. 15203276 Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. 15116424 Wepierre J, Marty JP, Chanal JL, Sincholle D: Percutaneous absorption of 5-iodo-2' deoxycytidine in the hairless rat and in man. Eur J Drug Metab Pharmacokinet. 1984 Jan-Mar;9(1):79-83. 6714272 Coral S, Sigalotti L, Altomonte M, Engelsberg A, Colizzi F, Cattarossi I, Maraskovsky E, Jager E, Seliger B, Maio M: 5-aza-2'-deoxycytidine-induced expression of functional cancer testis antigens in human renal cell carcinoma: immunotherapeutic implications. Clin Cancer Res. 2002 Aug;8(8):2690-5. 12171902 Olivares J, Verdys M: Isocratic high-performance liquid chromatographic method for studying the metabolism of blood plasma pyrimidine nucleosides and bases: concentration and radioactivity measurements. J Chromatogr. 1988 Dec 29;434(1):111-21. 3243806 Maley, F. et al., J. Biol. Chem., 1958, 233, 1538-1543, (5-diphosphate) Charubala, R. et al., Synthesis, 1984, 965-968, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl) Schaller, H. et al., J.A.C.S., 1963, 85, 3821-3827, (5'-(4,4'-dimethoxytrityl) 4N-benzoyl) Benz, E. et al., J.O.C., 1965, 30, 3067-3071, (4N-benzoyl, 5'-tosyl, 3',4N-dibenzoyl, 4N,5'-dibenzoyl, 5'-tosyl 4N-benzoyl, 5'-trityl 3',4N-dibenzoyl) Hruska, F.E. et al., Can. J. Chem., 1974, 52, 497-508, (pmr) Jones, A.J. et al., Proc. Natl. Acad. Sci. U.S.A., 1970, 65, 27-30, CA, 72, 96682j, (cmr) Miles, H.T., J.A.C.S., 1963, 85, 1007-1008, (ir, pmr) Young, D.W. et al., Acta Cryst. B, 1975, 31, 961-965, (cryst struct) Michelson, A.M. et al., J.C.S., 1954, 34-40, (phosphates, 3',4N-di-Ac, 5'-trityl, 5'-trityl 3',4N-di-Ac) Lewis, R.J., Sax's Dangerous Properties of Industrial Materials, 8th edn., Van Nostrand Reinhold, 1992, DAQ850 Aldrich Library of 13C and 1H FT NMR Spectra, 1992, 3, 396A, 396C, (nmr) Stawinski, J. et al., Chem. Comm., 1976, 243-244, (3',4N,5'-tribenzoyl) Ulbricht TL. Nucleosides. 3. Synthesis of 1-methyl-2'-deoxycytidine, and comments on the N.m.r. spectra of cytosine nucleosides. J Chem Soc Perkin 1. 1965 Sep:6134-5. Wang Z, Prudhomme DR, Buck JR, Park M, Rizzo CJ. Stereocontrolled syntheses of deoxyribonucleosides via photoinduced electron-transfer deoxygenation of benzoyl-protected ribo- and arabinonucleosides. J Org Chem. 2000 Sep 22;65(19):5969-85. Saneyoshi M, Tohyama J, Nakayama C, Takiya S, Iwabuchi M. Inhibitory effects of 3'deoxycytidine 5'-triphosphate and 3'-deoxyuridine 5'-triphosphate on DNA-dependent RNA polymerases I and II purified from Dictyostelium discoideum cells. Nucleic Acids Res. 1981 Jul 10;9(13):3129-38. FOX JJ, WEMPEN I. Pyrimidine nucleosides. Adv Carbohydr Chem. 1959;14:283-380. Raffaele Saladino, Enrico Mincione, Claudia Crestini, Maurizio Mezzetti. Transformations of thiopyrimidine and thiopurine nucleosides following oxidation with dimethyldioxirane. Tetrahedron, 1996, 52, 6759-6780 Aldrich Library of FT-IR Spectra, 1st edn., 1985, 2, 832B, 838D, 839C, (ir) Yang, J.T. et al., CA, 1966, 65, 12454, (ord) 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. http://hmdb.ca/system/metabolites/msds/000/000/008/original/HMDB00014.pdf?1358461423 Protein ushA P07024 USHA_ECOLI ushA http://ecmdb.ca/proteins/P07024.xml Multifunctional protein surE P0A840 SURE_ECOLI surE http://ecmdb.ca/proteins/P0A840.xml 5'-nucleotidase yjjG P0A8Y1 YJJG_ECOLI yjjG http://ecmdb.ca/proteins/P0A8Y1.xml Cytidine deaminase P0ABF6 CDD_ECOLI cdd http://ecmdb.ca/proteins/P0ABF6.xml Class B acid phosphatase P0AE22 APHA_ECOLI aphA http://ecmdb.ca/proteins/P0AE22.xml 5'-nucleotidase yfbR P76491 YFBR_ECOLI yfbR http://ecmdb.ca/proteins/P76491.xml Nucleoside permease nupC P0AFF2 NUPC_ECOLI nupC http://ecmdb.ca/proteins/P0AFF2.xml Nucleoside permease nupG P0AFF4 NUPG_ECOLI nupG http://ecmdb.ca/proteins/P0AFF4.xml Nucleoside permease nupX P33021 NUPX_ECOLI nupX http://ecmdb.ca/proteins/P33021.xml Nucleoside-specific channel-forming protein tsx P0A927 TSX_ECOLI tsx http://ecmdb.ca/proteins/P0A927.xml dCMP + Water > Deoxycytidine + Phosphate Deoxycytidine + Hydrogen ion + Water > Deoxyuridine + Ammonium dCMP + Water <> Deoxycytidine + Phosphate R01664 RXN0-5292 Deoxycytidine + Water <> Deoxyuridine + Ammonia R02485 Water + Deoxycytidine > Ammonia + Deoxyuridine R02485 CYTIDEAM-RXN Cytidine + Water + Deoxycytidine <> Uridine + Ammonia + Deoxyuridine R01878