Record Information
Version2.0
Creation Date2012-05-31 13:48:09 -0600
Update Date2015-06-03 15:53:52 -0600
Secondary Accession Numbers
  • ECMDB01245
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 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.
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
Weight:Average: 387.177
Monoisotopic: 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
DescriptionThis compound belongs to the class of chemical entities known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganic oxoanionic compounds
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Alkyl phosphate
  • Imidolactam
  • Oxolane
  • Heteroaromatic compound
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Organic oxide
  • Alcohol
  • Primary amine
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic 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:
SMPDB Pathways:
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
KEGG Pathways:
EcoCyc Pathways:
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
Concentrations
Not Available
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
Uniprot ID:
P00452
Molecular weight:
85774
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
Uniprot ID:
P0A6I0
Molecular weight:
24746
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
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
ATP + uridine = ADP + UMP
Gene Name:
udk
Uniprot ID:
P0A8F4
Molecular weight:
24353
Reactions
ATP + uridine = ADP + UMP.
ATP + cytidine = ADP + CMP.
General function:
Involved in electron carrier activity
Specific function:
Efficient electron donor for the essential enzyme ribonucleotide reductase. Is also able to reduce the interchain disulfide bridges of insulin
Gene Name:
trxC
Uniprot ID:
P0AGG4
Molecular weight:
15555
Reactions
Protein dithiol + NAD(P)(+) = protein disulfide + NAD(P)H.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2F contains the tyrosyl radical required for catalysis
Gene Name:
nrdF
Uniprot ID:
P37146
Molecular weight:
36443
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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. R1E contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide
Gene Name:
nrdE
Uniprot ID:
P39452
Molecular weight:
80478
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
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
Uniprot ID:
P69441
Molecular weight:
23586
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
Uniprot ID:
P69924
Molecular weight:
43517
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
Uniprot ID:
P0AC69
Molecular weight:
12879
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
Uniprot ID:
P0AC62
Molecular weight:
9137
General function:
Involved in protein binding
Specific function:
Involved in reducing some disulfides in a coupled system with glutathione reductase. Does not act as hydrogen donor for ribonucleotide reductase
Gene Name:
grxB
Uniprot ID:
P0AC59
Molecular weight:
24350
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:
grxA
Uniprot ID:
P68688
Molecular weight:
9685
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
Uniprot ID:
P0AA25
Molecular weight:
11807

Transporters

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
Uniprot ID:
P0A763
Molecular weight:
15463
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.