2.0 2012-05-31 13:48:09 -0600 2015-06-03 15:53:52 -0600 ECMDB01245 M2MDB000307 dCDP dCDP or Deoxycytidine 5'-diphosphate (dCDP) is a nucleoside diphosphate. It is related to the common nucleic acid CTP, or cytidine triphosphate, with the -OH (hydroxyl) group on the 2' carbon on the nucleotide's pentose removed (hence the deoxy- part of the name), and with one fewer phosphoryl group than CTP .dCDP is a product and competitive inhibitor of ribonucleoside-diphosphate reductase (EC 1.17.4.1) from Escherichia coli. Structural studies indicate the base is in anti conformation and the sugar in S-type puckering, when bound either to the complete enzyme complex or to the large protein subunit alone. [PMID: 8019775] Ribonucleoside-diphosphate reductase is very tightly controlled by a variety of allosteric effectors. The enzyme has different regions of it that act differently on allosteric regulators. At the activity site, dATP is a general inhibitor for all substrates and ATP is an activator. Binding of nucleotides at the specificity site further controls the activity of the enzyme towards different substrates in order to maintain an appropriate balance of all deoxynucleotides for DNA synthesis. The dNDPs produced by the enzyme are then phosphorylated to dNTPs by kinases. 2'-Deoxy-Cytidine 5'-pyrophosphate 2'-Deoxy-cytidine 5'-pyrophosphoric acid 2'-Deoxy-Cytidine pyrophosphate 2'-Deoxy-cytidine pyrophosphoric acid 2'-Deoxycytidine 5'-(trihydrogen diphosphate) 2'-Deoxycytidine 5'-(trihydrogen diphosphoric acid) 2'-Deoxycytidine 5'-diphosphate 2'-Deoxycytidine 5'-diphosphoric acid 2'-Deoxycytidine diphosphate 2'-Deoxycytidine diphosphoric acid 2'-Deoxycytidine-5'-diphosphate 2'-Deoxycytidine-5'-diphosphoric acid 2-Deoxycytidine 5-diphosphate 2-Deoxycytidine 5-diphosphoric acid 2-Deoxycytidine diphosphate 2-Deoxycytidine diphosphoric acid 4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-b-δ-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-β-D-erythro-pentofuranosyl]-2(1H)-pyrimidinone 4-amino-1-[2-Deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-β-δ-erythro-pentofuranosyl]-2(1H)-pyrimidinone D-1b-Ribofuranosylcytosine diphosphate D-1b-Ribofuranosylcytosine diphosphoric acid D-1beta-Ribofuranosylcytosine diphosphate D-1beta-Ribofuranosylcytosine diphosphoric acid D-1β-Ribofuranosylcytosine diphosphate D-1β-Ribofuranosylcytosine diphosphoric acid DCDP delta-1b-Ribofuranosylcytosine diphosphate delta-1b-Ribofuranosylcytosine diphosphoric acid Delta-1beta-Ribofuranosylcytosine diphosphate delta-1beta-Ribofuranosylcytosine diphosphoric acid Deoxy-CDP Deoxycytidine 5'-diphosphate Deoxycytidine 5'-diphosphoric acid Deoxycytidine diphosphate Deoxycytidine diphosphoric acid Deoxycytidine-diphosphate Deoxycytidine-diphosphoric acid δ-1b-Ribofuranosylcytosine diphosphate δ-1b-Ribofuranosylcytosine diphosphoric acid δ-1β-Ribofuranosylcytosine diphosphate δ-1β-Ribofuranosylcytosine diphosphoric acid C9H15N3O10P2 387.177 387.023266739 [({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid dCDP 800-73-7 NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1 InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 FTDHDKPUHBLBTL-SHYZEUOFSA-N Solid Cytosol logp -1.48 ALOGPS logs -1.53 ALOGPS solubility 1.13e+01 g/l ALOGPS logp -2.6 ChemAxon pka_strongest_acidic 1.79 ChemAxon pka_strongest_basic 0.3 ChemAxon iupac [({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid ChemAxon average_mass 387.177 ChemAxon mono_mass 387.023266739 ChemAxon smiles NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1 ChemAxon formula C9H15N3O10P2 ChemAxon inchi InChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 ChemAxon inchikey FTDHDKPUHBLBTL-SHYZEUOFSA-N ChemAxon polar_surface_area 201.44 ChemAxon refractivity 74.78 ChemAxon polarizability 30.77 ChemAxon rotatable_bond_count 6 ChemAxon acceptor_count 10 ChemAxon donor_count 5 ChemAxon physiological_charge -2 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 Metabolic pathways eco01100 pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I PWY0-166 Specdb::CMs 25964 Specdb::CMs 37992 Specdb::CMs 130573 Specdb::CMs 138307 Specdb::NmrOneD 8962 Specdb::NmrOneD 8963 Specdb::NmrOneD 8964 Specdb::NmrOneD 8965 Specdb::NmrOneD 8966 Specdb::NmrOneD 8967 Specdb::NmrOneD 8968 Specdb::NmrOneD 8969 Specdb::NmrOneD 8970 Specdb::NmrOneD 8971 Specdb::NmrOneD 8972 Specdb::NmrOneD 8973 Specdb::NmrOneD 8974 Specdb::NmrOneD 8975 Specdb::NmrOneD 8976 Specdb::NmrOneD 8977 Specdb::NmrOneD 8978 Specdb::NmrOneD 8979 Specdb::NmrOneD 8980 Specdb::NmrOneD 8981 Specdb::MsMs 27746 Specdb::MsMs 27747 Specdb::MsMs 27748 Specdb::MsMs 34304 Specdb::MsMs 34305 Specdb::MsMs 34306 Specdb::MsMs 439044 Specdb::MsMs 440125 Specdb::MsMs 447974 Specdb::MsMs 447975 Specdb::MsMs 2236412 Specdb::MsMs 2236952 Specdb::MsMs 2238514 Specdb::MsMs 2239086 Specdb::MsMs 2241212 Specdb::MsMs 2304486 Specdb::MsMs 2304487 Specdb::MsMs 2304488 Specdb::MsMs 3061808 Specdb::MsMs 3061809 Specdb::MsMs 3061810 HMDB01245 150855 132961 C00705 28846 DCDP YYY Deoxycytidine diphosphate 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 Allard, P., Kuprin, S., Ehrenberg, A. (1994). "Conformation of dCDP bound to protein R1 of Escherichia coli ribonucleotide reductase." J Magn Reson B 103:242-246. 8019775 Chiu TH, Morimoto H, Baker JJ: Biosynthesis and characterization of phosphatidylglycerophosphoglycerol, a possible intermediate in lipoteichoic acid biosynthesis in Streptococcus sanguis. Biochim Biophys Acta. 1993 Feb 24;1166(2-3):222-8. 8443240 Nara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp. Ribonucleoside-diphosphate reductase 1 subunit alpha P00452 RIR1_ECOLI nrdA http://ecmdb.ca/proteins/P00452.xml Cytidylate kinase P0A6I0 KCY_ECOLI cmk http://ecmdb.ca/proteins/P0A6I0.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Uridine kinase P0A8F4 URK_ECOLI udk http://ecmdb.ca/proteins/P0A8F4.xml Thioredoxin-2 P0AGG4 THIO2_ECOLI trxC http://ecmdb.ca/proteins/P0AGG4.xml Ribonucleoside-diphosphate reductase 2 subunit beta P37146 RIR4_ECOLI nrdF http://ecmdb.ca/proteins/P37146.xml Ribonucleoside-diphosphate reductase 2 subunit alpha P39452 RIR3_ECOLI nrdE http://ecmdb.ca/proteins/P39452.xml Adenylate kinase P69441 KAD_ECOLI adk http://ecmdb.ca/proteins/P69441.xml Ribonucleoside-diphosphate reductase 1 subunit beta P69924 RIR2_ECOLI nrdB http://ecmdb.ca/proteins/P69924.xml Glutaredoxin-4 P0AC69 GLRX4_ECOLI grxD http://ecmdb.ca/proteins/P0AC69.xml Glutaredoxin-3 P0AC62 GLRX3_ECOLI grxC http://ecmdb.ca/proteins/P0AC62.xml Glutaredoxin-2 P0AC59 GLRX2_ECOLI grxB http://ecmdb.ca/proteins/P0AC59.xml Glutaredoxin-1 P68688 GLRX1_ECOLI grxA http://ecmdb.ca/proteins/P68688.xml Thioredoxin-1 P0AA25 THIO_ECOLI trxA http://ecmdb.ca/proteins/P0AA25.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml CDP + Reduced Thioredoxin > dCDP + Water + Oxidized Thioredoxin CDP + glutaredoxin > dCDP + glutaredoxin + Water Adenosine triphosphate + dCDP <> ADP + dCTP R02326 DCDPKIN-RXN Adenosine triphosphate + dCMP <> ADP + dCDP R01665 RXN-11831 dCDP + Thioredoxin disulfide + Water <> Thioredoxin + CDP R02024 dCTP + Uridine <> dCDP + Uridine 5'-monophosphate R02327 dCTP + Cytidine <> dCDP + Cytidine monophosphate R02371 dCDP + Adenosine triphosphate > dCTP + ADP DCDPKIN-RXN Adenosine triphosphate + dCMP ADP + dCDP RXN-11831 Adenosine triphosphate + dCMP > ADP + dCDP Adenosine triphosphate + dCMP + Uridine 5'-monophosphate <> ADP + dCDP + Uridine 5'-diphosphate R00512 R01665 dCDP + Adenosine triphosphate > Adenosine diphosphate + dCTP + ADP PW_R003536 CDP + a reduced NrdH glutaredoxin-like protein > Water + dCDP + an oxidized NrdH glutaredoxin-like protein PW_R003544 CDP + reduced thioredoxin > Water + oxidized thioredoxin + dCDP PW_R003535