Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000307
Identification
Name: dCDP
Description: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 Pseudomonas aeruginosa. 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.
Structure
Thumb
Synonyms:
  • 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
Chemical Formula: C9H15N3O10P2
Average Molecular Weight: 387.177
Monoisotopic Molecular Weight: 387.023266739
InChI Key: FTDHDKPUHBLBTL-SHYZEUOFSA-N
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
CAS number: 800-73-7
IUPAC Name:[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
Traditional IUPAC Name: dCDP
SMILES:NC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct Parent Pyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility11.3 mg/mLALOGPS
logP-1.5ALOGPS
logP-3ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
pKa (Strongest Basic)-0.005ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.78 m3·mol-1ChemAxon
Polarizability30.77 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-e584f4f2cb1a8a01a7e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3910000000-d34603d21a6d1d52ae1fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-52ac41f181e1d5fbf96aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-4209000000-ea241dab90201ce7963eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9601000000-55120f468bf1ebba66cdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-bd81788fb13a599a4f60View in MoNA
References
References:
  • 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. Pubmed: 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. Pubmed: 8443240
  • 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. Pubmed: 22080510
  • 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. Pubmed: 21097882
  • 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. Pubmed: 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. Pubmed: 18331064
Synthesis Reference: Nara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID28846
HMDB IDHMDB01245
Pubchem Compound ID150855
Kegg IDC00705
ChemSpider ID132961
WikipediaDeoxycytidine diphosphate
BioCyc IDDCDP
EcoCyc IDDCDP
Ligand ExpoYYY

Enzymes

General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
Gene Name:
nrdA
Locus Tag:
PA1156
Molecular weight:
107.1 kDa
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in cytidylate kinase activity
Specific function:
ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors
Gene Name:
cmk
Locus Tag:
PA3163
Molecular weight:
24.6 kDa
Reactions
ATP + (d)CMP = ADP + (d)CDP.
General function:
Involved in nucleoside diphosphate kinase activity
Specific function:
Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate
Gene Name:
ndk
Locus Tag:
PA3807
Molecular weight:
15.6 kDa
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Locus Tag:
PA3686
Molecular weight:
23.1 kDa
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Gene Name:
nrdB
Locus Tag:
PA1155
Molecular weight:
47.4 kDa
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Locus Tag:
PA3533
Molecular weight:
11.8 kDa
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxC
Locus Tag:
PA5129
Molecular weight:
9.2 kDa
General function:
Involved in electron carrier activity
Specific function:
Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
Gene Name:
trxA
Locus Tag:
PA5240
Molecular weight:
11.9 kDa