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Identification
YMDB IDYMDB00916
NamedCDP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptiondCDP, also known as deoxy-CDP, 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. dCDP is an extremely weak basic (essentially neutral) compound (based on its pKa). dCDP exists in all living species, ranging from bacteria to humans.
Structure
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Synonyms
  • 2'-deoxy-Cytidine 5'-pyrophosphate
  • 2'-deoxy-Cytidine pyrophosphate
  • 2'-Deoxycytidine 5'-diphosphate
  • 2'-Deoxycytidine diphosphate
  • 2'-Deoxycytidine-5'-diphosphate
  • 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
  • D-1beta-Ribofuranosylcytosine diphosphate
  • dCDP
  • delta-1beta-Ribofuranosylcytosine diphosphate
  • Deoxy-CDP
  • Deoxycytidine 5'-diphosphate
  • Deoxycytidine diphosphate
  • 2'-Deoxycytidine 5'-diphosphoric acid
  • 2'-Deoxycytidine diphosphoric acid
  • D-1b-Ribofuranosylcytosine diphosphate
  • D-1b-Ribofuranosylcytosine diphosphoric acid
  • D-1beta-Ribofuranosylcytosine diphosphoric acid
  • D-1Β-ribofuranosylcytosine diphosphate
  • D-1Β-ribofuranosylcytosine diphosphoric acid
  • Deoxycytidine diphosphoric acid
CAS number800-73-7
WeightAverage: 387.177
Monoisotopic: 387.023266739
InChI KeyFTDHDKPUHBLBTL-SHYZEUOFSA-N
InChIInChI=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
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 NamedCDP
Chemical FormulaC9H15N3O10P2
SMILES[H]O[C@@]1([H])C([H])([H])[C@@]([H])(O[C@]1([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility11.3 g/LALOGPS
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 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
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
dCDP + Adenosine triphosphateADP + dCTP
CDP + reduced thioredoxin → water + oxidized thioredoxin + dCDP
CDP + a reduced NrdH glutaredoxin-like protein → water + dCDP + an oxidized NrdH glutaredoxin-like protein
KEGG Reactions
Adenosine triphosphate + dCMPdCDP + ADP
Adenosine triphosphate + dCDPADP + dCTP
thioredoxin dithiol + CDPdCDP + thioredoxin disulfide + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-002e-7912000000-ef0991eaee32b505e016JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0006-9851100000-62426a0730b483cea09bJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0570-9418000000-2d9af3073a3dc2deba5dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-056r-9511000000-84defb0c7de79c169ebfJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0409000000-e5af2ab8466aa7c560d3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-e584f4f2cb1a8a01a7e7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3910000000-d34603d21a6d1d52ae1fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-52ac41f181e1d5fbf96aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-4209000000-ea241dab90201ce7963eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9601000000-55120f468bf1ebba66cdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-bd81788fb13a599a4f60JSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Jong, A. Y., Ma, J. J. (1991). "Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity." Arch Biochem Biophys 291:241-246.1659321
Synthesis Reference:Nara, Takashi; Misawa, Masanaru. Bacterial phosphorylation of 5'-deoxycytidine monophosphate to di-or triphosphate. Jpn. Tokkyo Koho (1971), 2 pp.
External Links:
ResourceLink
CHEBI ID28846
HMDB IDHMDB01245
Pubchem Compound ID150855
Kegg IDC00705
ChemSpider ID24785482
FOODB IDFDB022510
WikipediaDeoxycytidine_triphosphate
BioCyc IDDCDP

Enzymes

General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:
RNR2
Uniprot ID:
P09938
Molecular weight:
46147.0
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
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. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
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
Gene Name:
RNR1
Uniprot ID:
P21524
Molecular weight:
99560.20313
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.