Record Information
Version1.0
Creation date2011-09-21 00:15:07 UTC
Update date2020-09-17 15:38:52 UTC
Primary IDFDB022510
Secondary Accession NumbersNot Available
Chemical Information
FooDB NamedCDP
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. Within humans, dCDP participates in a number of enzymatic reactions. In particular, dCDP can be biosynthesized from CDP through the action of the enzyme ribonucleoside-diphosphate reductase large subunit. In addition, dCDP can be converted into dCTP; which is mediated by the enzyme nucleoside diphosphate kinase 6. In humans, dCDP is involved in pyrimidine metabolism. Outside of the human body, dCDP has been detected, but not quantified in, several different foods, such as climbing beans, fox grapes, chinese mustards, angelica, and guava. This could make dCDP a potential biomarker for the consumption of these foods. A 2'-deoxycytidine phosphate that is the 2'- deoxy derivative of cytidine 5'-diphosphate (CDP).
CAS Number800-73-7
Structure
Thumb
Synonyms
SynonymSource
2'-Deoxycytidine 5'-diphosphateChEBI
2'-Deoxycytidine diphosphateChEBI
D-1beta-Ribofuranosylcytosine diphosphateChEBI
Deoxycytidine diphosphateChEBI
2'-Deoxycytidine 5'-diphosphoric acidGenerator
2'-Deoxycytidine diphosphoric acidGenerator
D-1b-Ribofuranosylcytosine diphosphateGenerator
D-1b-Ribofuranosylcytosine diphosphoric acidGenerator
D-1beta-Ribofuranosylcytosine diphosphoric acidGenerator
D-1Β-ribofuranosylcytosine diphosphateGenerator
D-1Β-ribofuranosylcytosine diphosphoric acidGenerator
Deoxycytidine diphosphoric acidGenerator
2'-Deoxy-cytidine 5'-pyrophosphateHMDB
2'-Deoxy-cytidine pyrophosphateHMDB
2'-Deoxycytidine-5'-diphosphateHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
4-Amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
delta-1beta-Ribofuranosylcytosine diphosphateHMDB
Deoxy-CDPHMDB
Deoxycytidine 5'-diphosphateHMDB
2'-Deoxy-cytidine 5'-pyroateHMDB
2'-deoxy-Cytidine 5'-pyrophosphatehmdb
2'-Deoxy-cytidine pyroateHMDB
2'-deoxy-Cytidine pyrophosphatehmdb
2'-Deoxycytidine 5'-diateChEBI
2'-Deoxycytidine 5'-diic acidGenerator
2'-Deoxycytidine diateChEBI
2'-Deoxycytidine diic acidGenerator
2'-Deoxycytidine-5'-diateHMDB
4-amino-1-[2-Deoxy-5-O-[hydroxy(onooxy)inyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
4-amino-1-[2-Deoxy-5-O-[hydroxy(onooxy)inyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinoneHMDB
4-amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-D-erythro-pentofuranosyl]-2(1H)-pyrimidinonehmdb
4-amino-1-[2-deoxy-5-O-[hydroxy(phosphonooxy)phosphinyl]-beta-delta-erythro-pentofuranosyl]-2(1H)-pyrimidinonehmdb
D-1b-Ribofuranosylcytosine diateGenerator
D-1b-Ribofuranosylcytosine diic acidGenerator
D-1beta-Ribofuranosylcytosine diateChEBI
D-1beta-Ribofuranosylcytosine diic acidGenerator
D-1β-ribofuranosylcytosine diateGenerator
D-1β-ribofuranosylcytosine diic acidGenerator
dCDPhmdb
delta-1beta-Ribofuranosylcytosine diateHMDB
Deoxycytidine 5'-diateHMDB
Deoxycytidine diateChEBI
Deoxycytidine diic acidGenerator
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H15N3O10P2
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
InChI IdentifierInChI=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
InChI KeyFTDHDKPUHBLBTL-SHYZEUOFSA-N
Isomeric SMILESNC1=NC(=O)N(C=C1)[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1
Average Molecular Weight387.177
Monoisotopic Molecular Weight387.023266739
Classification
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
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSdCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-002e-7912000000-ef0991eaee32b505e016Spectrum
Predicted GC-MSdCDP, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0006-9851100000-62426a0730b483cea09bSpectrum
Predicted GC-MSdCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSdCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0570-9418000000-2d9af3073a3dc2deba5dSpectrum
MS/MSLC-MS/MS Spectrum - , negativesplash10-056r-9511000000-84defb0c7de79c169ebfSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0409000000-e5af2ab8466aa7c560d3Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39Spectrum
MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-4aa3ce1bf37251d7fc83Spectrum
MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-056r-9435000000-55592321586c623c4830Spectrum
MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0a4i-0903000000-1de5fa4ac24e19830f39Spectrum
MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-056r-9411000000-84bbde6c497548c746d1Spectrum
MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-63f9c6b289fb024c58faSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-e584f4f2cb1a8a01a7e7Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3910000000-d34603d21a6d1d52ae1fSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-52ac41f181e1d5fbf96aSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-4209000000-ea241dab90201ce7963eSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9601000000-55120f468bf1ebba66cdSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-bd81788fb13a599a4f60Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0900000000-63028e00ccb9887f46f5Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-1900000000-9b943638c706a10be8dbSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-3910000000-f5ebfcca0e4ec5d76afaSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0409000000-47d71d5707b30d7b3ad5Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9324000000-25bfbc45e3248b83b219Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-a5e502a2627af2048a1fSpectrum
NMRNot Available
ChemSpider ID132961
ChEMBL IDNot Available
KEGG Compound IDC00705
Pubchem Compound ID150855
Pubchem Substance IDNot Available
ChEBI ID28846
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB01245
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID50858
KNApSAcK IDNot Available
HET IDYYY
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDDeoxycytidine diphosphate
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
Enzymes
NameGene NameUniProt ID
Uridine-cytidine kinase-like 1UCKL1Q9NWZ5
UMP-CMP kinase 2, mitochondrialCMPK2Q5EBM0
Ribonucleoside-diphosphate reductase large subunitRRM1P23921
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046 map00240
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference