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Showing Compound CDP (FDB022683)

Record Information
Version1.0
Creation date2011-09-21 00:17:53 UTC
Update date2020-09-17 15:41:54 UTC
Primary IDFDB022683
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameCDP
DescriptionCDP, also known as 5'-CDP, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. CDP is an extremely weak basic (essentially neutral) compound (based on its pKa). CDP exists in all living species, ranging from bacteria to humans. In humans, CDP is involved in cardiolipin biosynthesis. Outside of the human body, CDP has been detected, but not quantified in, several different foods, such as carobs, mexican oregano, evergreen huckleberries, green vegetables, and pepper (c. baccatum). This could make CDP a potential biomarker for the consumption of these foods.
CAS Number63-38-7
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
SynonymSource
5'-CDPChEBI
Cytidine 5'-diphosphateChEBI
Cytidine 5'-diphosphoric acidChEBI
Cytidine 5'-pyrophosphateChEBI
Cytidine diphosphateChEBI
Cytidine, 5'-(trihydrogen pyrophosphate)ChEBI
CYTIDINE-5'-diphosphATEChEBI
Cytidine 5'-pyrophosphoric acidGenerator
Cytidine diphosphoric acidGenerator
Cytidine, 5'-(trihydrogen pyrophosphoric acid)Generator
CYTIDINE-5'-diphosphoric acidGenerator
Cytidine-diphosphateHMDB
Diphosphate, cytidineHMDB
CDPhmdb
Cytidine 5'-diateChEBI
Cytidine 5'-diic acidGenerator
Cytidine 5'-dioric acidChEBI
Cytidine 5'-pyroateChEBI
Cytidine 5'-pyroic acidGenerator
Cytidine diateChEBI
Cytidine diic acidGenerator
CYTIDINE-5'-diATEChEBI
CYTIDINE-5'-diic acidGenerator
cytidine-5'-diphosphatehmdb
Cytidine-diateHMDB
cytidine-diphosphatehmdb
Cytidine, 5'-(trihydrogen pyroate)ChEBI
Cytidine, 5'-(trihydrogen pyroic acid)Generator
Predicted Properties
PropertyValueSource
Water Solubility10.1 g/LALOGPS
logP-1.4ALOGPS
logP-3.3ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
pKa (Strongest Basic)-0.033ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area221.67 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity76.29 m³·mol⁻¹ChemAxon
Polarizability31.39 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC9H15N3O11P2
IUPAC name[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
InChI IdentifierInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChI KeyZWIADYZPOWUWEW-XVFCMESISA-N
Isomeric SMILESNC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
Average Molecular Weight403.1764
Monoisotopic Molecular Weight403.018181361
Classification
Description Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • Pentose-5-phosphate
  • Pentose phosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

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-MSCDP, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004i-5923000000-f7e7b227d8dab9e29e4bSpectrum
Predicted GC-MSCDP, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00di-3209010000-ff27ee45250db3e35193Spectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-9000000000-f5d958a3ccf576052a6bSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-00di-0390000000-0274cdf4190792442001Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0udi-0009000000-2c8a9272dc29076a6167Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9602700000-4b46ddc9506634a02dc5Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-0a4i-0059000000-d598d99a604dda402181Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0003900000-69398917fb0c37a4304fSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0zg0-0726900000-8d967e8ca6677a467fb8Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0901000000-6aed044cc4135aa261dfSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3900000000-92fac6a8baf47bac3014Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-5ad7bca4dc732a0e3840Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0903300000-44d24cfda26f8f0a8d96Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9701000000-d96a23308bcfcf9cf55fSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d7e0d2a5e8d20180b483Spectrum
NMRNot Available
ChemSpider ID5902
ChEMBL IDCHEMBL425252
KEGG Compound IDC00112
Pubchem Compound ID6132
Pubchem Substance IDNot Available
ChEBI ID17239
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB01546
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG ID33901
KNApSAcK IDNot Available
HET IDCDP
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDCDP
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
UMP-CMP kinase 2, mitochondrialCMPK2Q5EBM0
Ribonucleoside-diphosphate reductase large subunitRRM1P23921
Polyribonucleotide nucleotidyltransferase 1, mitochondrialPNPT1Q8TCS8
Dolichol kinaseDOLKQ9UPQ8
Nucleoside diphosphate kinaseNME4A2IDD0
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