Record Information
Version1.0
Creation Date2016-09-30 22:47:29 UTC
Update Date2020-05-21 16:29:27 UTC
BMDB IDBMDB0001546
Secondary Accession Numbers
  • BMDB01546
Metabolite Identification
Common 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. CDP is an extremely weak basic (essentially neutral) compound (based on its pKa). CDP exists in all living species, ranging from bacteria to humans.
Structure
Thumb
Synonyms
ValueSource
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
Chemical FormulaC9H15N3O11P2
Average Molecular Weight403.1764
Monoisotopic Molecular Weight403.018181361
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
Traditional NameCDP
CAS Registry Number63-38-7
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
InChI Identifier
InChI=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
Chemical Taxonomy
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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP2.44HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-5923000000-f7e7b227d8dab9e29e4bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00di-3209010000-ff27ee45250db3e35193View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-9000000000-f5d958a3ccf576052a6bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-00di-0390000000-0274cdf4190792442001View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0udi-0009000000-2c8a9272dc29076a6167View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9602700000-4b46ddc9506634a02dc5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-0a4i-0059000000-d598d99a604dda402181View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0003900000-69398917fb0c37a4304fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0zg0-0726900000-8d967e8ca6677a467fb8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0k9i-0927400000-86e5ba01091f928ca88fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0kdi-9814400000-54042f12a186a46a5a17View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0k9i-0927400000-61338365caaf6cc96eddView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03di-0900000000-2e5da7181d5154fd5287View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-8913200000-d327869c80aa6b6ba8b7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-7913200000-4f2656e2010a4274c652View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-ae7cefa275aa112f8ff3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0000900000-1f74a916c1bec3408d2eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-056r-9601000000-0261d005e8d3964fc255View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-8913200000-3093e23d54c628f19ea0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0901000000-6aed044cc4135aa261dfView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3900000000-92fac6a8baf47bac3014View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-5ad7bca4dc732a0e3840View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0903300000-44d24cfda26f8f0a8d96View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9701000000-d96a23308bcfcf9cf55fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d7e0d2a5e8d20180b483View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0100900000-fd8a10c051d8566d4abcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9418200000-cd847d00773e220445ddView in MoNA
1D NMR1H NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
  • Nucleus
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001546
DrugBank IDDB04555
Phenol Explorer Compound IDNot Available
FooDB IDFDB022683
KNApSAcK IDNot Available
Chemspider ID5902
KEGG Compound IDC00112
BioCyc IDCDP
BiGG ID33901
Wikipedia LinkCytidine_diphosphate
METLIN ID6313
PubChem Compound6132
PDB IDNot Available
ChEBI ID17239
References
Synthesis ReferenceChambers, Robert Warner; Shapiro, Philip; Kurkov, Viktor. Synthesis of cytidine 5'-diphosphate and guanosine 5'-diphosphate. Journal of the American Chemical Society (1960), 82 970-5.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Lipid transport and metabolism
Specific function:
Functions in the biosynthesis of the anionic phospholipids phosphatidylglycerol and cardiolipin.
Gene Name:
PGS1
Uniprot ID:
Q2KJ28
Molecular weight:
62732.0
General function:
Lipid transport and metabolism
Specific function:
Catalyzes the conversion of phosphatidic acid (PA) to CDP-diacylglycerol (CDP-DAG), an essential intermediate in the synthesis of phosphatidylglycerol, cardiolipin and phosphatidylinositol (By similarity). Exhibits specificity for the nature of the acyl chains at the sn-1 and sn-2 positions in the substrate, PA and the preferred acyl chain composition is 1-stearoyl-2-arachidonoyl-sn-phosphatidic acid (By similarity). Plays an important role in regulating the growth and maturation of lipid droplets which are storage organelles at the center of lipid and energy homeostasis (By similarity).
Gene Name:
CDS2
Uniprot ID:
A0JNC1
Molecular weight:
51357.0
General function:
Involved in ADP-ribose diphosphatase activity
Specific function:
Hydrolyzes ADP-ribose, IDP-ribose, CDP-glycerol, CDP-choline and CDP-ethanolamine, but not other non-reducing ADP-sugars or CDP-glucose. May be involved in immune cell signaling as suggested by the second-messenger role of ADP-ribose, which activates TRPM2 as a mediator of oxidative/nitrosative stress (By similarity).
Gene Name:
ADPRM
Uniprot ID:
A7YY53
Molecular weight:
39235.0
General function:
Lipid transport and metabolism
Specific function:
Catalyzes phosphatidylcholine biosynthesis from CDP-choline. It thereby plays a central role in the formation and maintenance of vesicular membranes (By similarity).
Gene Name:
CHPT1
Uniprot ID:
Q1LZE6
Molecular weight:
45249.0
General function:
Involved in ethanolaminephosphotransferase activity
Specific function:
Catalyzes phosphatidylethanolamine biosynthesis from CDP-ethanolamine. It thereby plays a central role in the formation and maintenance of vesicular membranes. Involved in the foramtion of phosphatidylethanolamine via 'Kennedy' pathway (By similarity).
Gene Name:
SELENOI
Uniprot ID:
Q17QM4
Molecular weight:
45214.0
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Plays an important role in the biosynthesis of the phospholipid phosphatidylethanolamine. Catalyzes the formation of CDP-ethanolamine (By similarity).
Gene Name:
PCYT2
Uniprot ID:
Q5EA75
Molecular weight:
44158.0
General function:
Lipid transport and metabolism
Specific function:
Involved in the synthesis of the sugar donor Dol-P-Man which is required in the synthesis of N-linked and O-linked oligosaccharides and for that of GPI anchors.
Gene Name:
DOLK
Uniprot ID:
Q58CR4
Molecular weight:
59190.0
General function:
Nucleotide transport and metabolism
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 (By similarity).
Gene Name:
NME7
Uniprot ID:
Q5E9Y9
Molecular weight:
42599.0
Reactions
Cytidine triphosphate + ADP → CDP + Adenosine triphosphatedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
CANT1
Uniprot ID:
E1BGL5
Molecular weight:
44706.0
Reactions
Cytidine triphosphate + Water → CDP + Hydrogen phosphatedetails
CDP + Water → Cytidine monophosphate + Hydrogen phosphatedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
CMPK2
Uniprot ID:
F1N2W6
Molecular weight:
64396.0
Reactions
CDP + ADP → Cytidine monophosphate + Adenosine triphosphatedetails
General function:
Not Available
Specific function:
Not Available
Gene Name:
RRM2
Uniprot ID:
E1BI58
Molecular weight:
44821.0
Reactions
CDP + thioredoxin disulfide + Water → dCDP + thioredoxindetails