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
DescriptiondCDP 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
Description belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganic oxoanionic compounds
Sub ClassOrganic pyrophosphates
Direct ParentOrganic pyrophosphates
Alternative Parents
Substituents
  • Organic pyrophosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Hydropyrimidine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Pyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • 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 g/LALOGPS
logP-1.5ALOGPS
logP-2.6ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)1.79ChemAxon
pKa (Strongest Basic)0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area201.44 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity74.78 m³·mol⁻¹ChemAxon
Polarizability30.77 ųChemAxon
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 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • pyrimidine deoxyribonucleotides de novo biosynthesis I PWY0-166
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-002e-7912000000-ef0991eaee32b505e016View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0006-9851100000-62426a0730b483cea09bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0570-9418000000-2d9af3073a3dc2deba5dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-056r-9511000000-84defb0c7de79c169ebfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0409000000-e5af2ab8466aa7c560d3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-4aa3ce1bf37251d7fc83View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-056r-9435000000-55592321586c623c4830View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-056r-9411000000-84bbde6c497548c746d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-63f9c6b289fb024c58faView in MoNA
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-63028e00ccb9887f46f5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-9b943638c706a10be8dbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3910000000-f5ebfcca0e4ec5d76afaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0409000000-47d71d5707b30d7b3ad5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9324000000-25bfbc45e3248b83b219View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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.