Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:10:45 UTC
HMDB IDHMDB01546
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP
DescriptionCytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate.
Structure
Thumb
Synonyms
  1. CDP
  2. Cytidine-5'-diphosphate
  3. Cytidine-diphosphate
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 IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxyphosphonic acid
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
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleotides
Sub ClassPyrimidine Ribonucleotides
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Ribonucleotides(KEGG)
  • cytidine 5'-phosphate(ChEBI)
  • pyrimidine ribonucleoside 5'-diphosphate(ChEBI)
Substituents
  • 1,2 Diol
  • Aminopyrimidine
  • Glycosyl Compound
  • Hydropyrimidine
  • Monosaccharide Phosphate
  • N Glycosyl Compound
  • Organic Hypophosphite
  • Organic Phosphite
  • Organic Pyrophosphate
  • Oxolane
  • Pentose Monosaccharide
  • Phosphoric Acid Ester
  • Pyrimidine
  • Pyrimidone
  • Saccharide
  • Secondary Alcohol
Direct ParentPyrimidine Ribonucleoside Diphosphates
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • 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
water solubility10.1 g/LALOGPS
logP-1.4ALOGPS
logP-3.6ChemAxon
logS-1.6ALOGPS
pKa (strongest acidic)1.77ChemAxon
pKa (strongest basic)-0.52ChemAxon
physiological charge-2ChemAxon
hydrogen acceptor count11ChemAxon
hydrogen donor count6ChemAxon
polar surface area221.67ChemAxon
rotatable bond count6ChemAxon
refractivity76.29ChemAxon
polarizability31.39ChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified36.0 +/- 12.0 uMAdult (>18 years old)BothNormal
  • Geigy Scient...
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022683
KNApSAcK IDNot Available
Chemspider ID5902
KEGG Compound IDC00112
BioCyc IDCDP
BiGG ID33901
Wikipedia LinkCDP
NuGOwiki LinkHMDB01546
Metagene LinkHMDB01546
METLIN ID6313
PubChem Compound6132
PDB IDCDP
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 References
  1. Houtkooper RH, Akbari H, van Lenthe H, Kulik W, Wanders RJ, Frentzen M, Vaz FM: Identification and characterization of human cardiolipin synthase. FEBS Lett. 2006 May 29;580(13):3059-64. Epub 2006 Apr 27. Pubmed: 16678169
  2. George TP, Cook HW, Byers DM, Palmer FB, Spence MW: Inhibition of phosphatidylcholine and phosphatidylethanolamine biosynthesis by cytochalasin B in cultured glioma cells: potential regulation of biosynthesis by Ca(2+)-dependent mechanisms. Biochim Biophys Acta. 1991 Jul 9;1084(2):185-93. Pubmed: 1854804
  3. Riekhof WR, Voelker DR: Uptake and utilization of lyso-phosphatidylethanolamine by Saccharomyces cerevisiae. J Biol Chem. 2006 Dec 1;281(48):36588-96. Epub 2006 Oct 2. Pubmed: 17015438
  4. Tsitolovskii LE, Kraevskii AA: [Possible relation between learning and non-template RNA synthesis in neurons]. Zh Vyssh Nerv Deiat Im I P Pavlova. 1982 Mar-Apr;32(2):284-91. Pubmed: 6178232
  5. Carstensen S, Pliska-Matyshak G, Bhuvarahamurthy N, Robbins KM, Murthy PP: Biosynthesis and localization of phosphatidyl-scyllo-inositol in barley aleurone cells. Lipids. 1999 Jan;34(1):67-73. Pubmed: 10188599
  6. Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 2005 Apr 11;579(10):2161-5. Pubmed: 15811335
  7. George TP, Morash SC, Cook HW, Byers DM, Palmer FB, Spence MW: Phosphatidylcholine biosynthesis in cultured glioma cells: evidence for channeling of intermediates. Biochim Biophys Acta. 1989 Aug 22;1004(3):283-91. Pubmed: 2758024
  8. Houtkooper RH, Vaz FM: Cardiolipin, the heart of mitochondrial metabolism. Cell Mol Life Sci. 2008 Aug;65(16):2493-506. doi: 10.1007/s00018-008-8030-5. Pubmed: 18425414
  9. Lindblad L, Schersten T: Incorporation rate in vitro of choline and methyl-methionine into human hepatic lecithins. Scand J Gastroenterol. 1976;11(6):587-91. Pubmed: 981963

Enzymes

Gene Name:
CMPK1
Uniprot ID:
P30085
Reactions
Adenosine triphosphate + Cytidine monophosphate unknown ADP + CDPdetails
Gene Name:
ENTPD1
Uniprot ID:
P49961
Reactions
CDP + Water unknown Cytidine monophosphate + Phosphoric aciddetails
Cytidine triphosphate + Water unknown CDP + Phosphoric aciddetails
Gene Name:
ENTPD3
Uniprot ID:
O75355
Reactions
CDP + Water unknown Cytidine monophosphate + Phosphoric aciddetails
Cytidine triphosphate + Water unknown CDP + Phosphoric aciddetails
Gene Name:
NME4
Uniprot ID:
O00746
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
RRM1
Uniprot ID:
P23921
Reactions
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDPdetails
Gene Name:
NME1
Uniprot ID:
P15531
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
NME7
Uniprot ID:
Q9Y5B8
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
RRM2
Uniprot ID:
P31350
Reactions
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDPdetails
Gene Name:
NME2
Uniprot ID:
P22392
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
NME3
Uniprot ID:
Q13232
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
NME6
Uniprot ID:
O75414
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails
Gene Name:
PFKP
Uniprot ID:
Q01813
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphatedetails
Gene Name:
PFKL
Uniprot ID:
P17858
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphatedetails
Gene Name:
PFKM
Uniprot ID:
P08237
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate unknown CDP + D-Tagatose 1,6-bisphosphatedetails
Gene Name:
PKM
Uniprot ID:
P14618
Gene Name:
PKLR
Uniprot ID:
P30613
Gene Name:
PNPT1
Uniprot ID:
Q8TCS8
Reactions
RNA + Phosphoric acid unknown RNA + CDPdetails
Gene Name:
RRM2B
Uniprot ID:
Q7LG56
Reactions
dCDP + Thioredoxin disulfide + Water unknown Thioredoxin + CDPdetails
Gene Name:
CMPK2
Uniprot ID:
Q5EBM0
Reactions
Adenosine triphosphate + Cytidine monophosphate unknown ADP + CDPdetails
Gene Name:
ENTPD8
Uniprot ID:
Q5MY95
Reactions
CDP + Water unknown Cytidine monophosphate + Phosphoric aciddetails
Cytidine triphosphate + Water unknown CDP + Phosphoric aciddetails
Gene Name:
NME2P1
Uniprot ID:
O60361
Gene Name:
NUDT18
Uniprot ID:
Q6ZVK8
Gene Name:
DOLK
Uniprot ID:
Q9UPQ8
Reactions
Cytidine triphosphate + dolichol unknown CDP + Dolichol-20details
Gene Name:
NME4
Uniprot ID:
A2IDD0
Gene Name:
NME5
Uniprot ID:
P56597
Reactions
Adenosine triphosphate + CDP unknown ADP + Cytidine triphosphatedetails