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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-20 20:21:48 UTC
HMDB IDHMDB0001546
Secondary Accession Numbers
  • HMDB01546
Metabolite Identification
Common NameCDP
DescriptionCdp, also known as cytidine 5'-diphosphate or 5'-cdp, is a member of the class of compounds known as pyrimidine ribonucleoside diphosphates. Pyrimidine ribonucleoside diphosphates are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. Cdp is soluble (in water) and a moderately acidic compound (based on its pKa). Cdp can be found primarily in blood. Within the cell, cdp is primarily located in the mitochondria and in the nucleus. Cdp exists in all living species, ranging from bacteria to humans. In humans, cdp is involved in the pyrimidine metabolism. Cdp is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate..
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, cytidineMeSH
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
DescriptionThis compound 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 phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyrimidine
  • Monosaccharide
  • Phosphoric acid ester
  • Hydropyrimidine
  • Imidolactam
  • Organic phosphoric acid derivative
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Amine
  • Alcohol
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary amine
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Process

Naturally occurring process:

  Biological process:

    Biochemical pathway:

Disposition

Biological location:

  Subcellular:

  Biofluid and excreta:

Source:

  Biological:

    Plant:

Route of exposure:

  Enteral:

Role

Industrial application:

  Pharmaceutical industry:

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 Area221.67 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity76.29 m³·mol⁻¹ChemAxon
Polarizability31.39 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
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
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
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
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Mitochondria
  • Nucleus
Biofluid Locations
  • Blood
Tissue LocationNot Available
Pathways
NameSMPDB/PathwhizKEGG
Beta Ureidopropionase DeficiencyPw000187Pw000187 greyscalePw000187 simpleNot Available
Dihydropyrimidinase DeficiencyPw000189Pw000189 greyscalePw000189 simpleNot Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)Pw000190Pw000190 greyscalePw000190 simpleNot Available
Pyrimidine MetabolismPw000160Pw000160 greyscalePw000160 simpleMap00240
UMP Synthase Deficiency (Orotic Aciduria)Pw000188Pw000188 greyscalePw000188 simpleNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified36.0 +/- 12.0 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022683
KNApSAcK IDNot Available
Chemspider ID5902
KEGG Compound IDC00112
BioCyc IDCDP
BiGG ID33901
Wikipedia LinkNot Available
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 ]

Only showing the first 10 proteins. There are 32 proteins in total.

Enzymes

General function:
Involved in calcium ion binding
Specific function:
Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP. Involved in proteoglycan synthesis.
Gene Name:
CANT1
Uniprot ID:
Q8WVQ1
Molecular weight:
44839.24
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. Inhibitor of p53-induced apoptosis.
Gene Name:
NME6
Uniprot ID:
O75414
Molecular weight:
22002.965
Reactions
Adenosine triphosphate + CDP → ADP + Cytidine triphosphatedetails
General function:
Involved in 3'-5'-exoribonuclease activity
Specific function:
RNA-binding protein implicated in numerous RNA metabolic processes. Hydrolyzes single-stranded polyribonucleotides processively in the 3'-to-5' direction. Mitochondrial intermembrane factor with RNA-processing exoribonulease activity. Component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Required for correct processing and polyadenylation of mitochondrial mRNAs. Plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. Plays a role in mitochondrial morphogenesis and respiration; regulates the expression of the electron transport chain (ETC) components at the mRNA and protein levels. In the cytoplasm, shows a 3'-to-5' exoribonuclease mediating mRNA degradation activity; degrades c-myc mRNA upon treatment with IFNB1/IFN-beta, resulting in a growth arrest in melanoma cells. Regulates the stability of specific mature miRNAs in melanoma cells; specifically and selectively degrades miR-221, preferentially. Plays also a role in RNA cell surveillance by cleaning up oxidized RNAs. Binds to the RNA subunit of ribonuclease P, MRP RNA and miR-221 microRNA.
Gene Name:
PNPT1
Uniprot ID:
Q8TCS8
Molecular weight:
85949.84
Reactions
RNA + Phosphoric acid → RNA + CDPdetails
General function:
Involved in oxidoreductase activity
Specific function:
Plays a pivotal role in cell survival by repairing damaged DNA in a p53/TP53-dependent manner. Supplies deoxyribonucleotides for DNA repair in cells arrested at G1 or G2. Contains an iron-tyrosyl free radical center required for catalysis. Forms an active ribonucleotide reductase (RNR) complex with RRM1 which is expressed both in resting and proliferating cells in response to DNA damage.
Gene Name:
RRM2B
Uniprot ID:
Q7LG56
Molecular weight:
48786.6
Reactions
dCDP + Thioredoxin disulfide + Water → Thioredoxin + CDPdetails
General function:
Involved in thymidylate kinase activity
Specific function:
May participate in dUTP and dCTP synthesis in mitochondria. Is able to phosphorylate dUMP, dCMP, CMP, UMP and monophosphates of the pyrimidine nucleoside analogs ddC, dFdC, araC, BVDU and FdUrd with ATP as phosphate donor. Efficacy is highest for dUMP followed by dCMP; CMP and UMP are poor substrates. May be involved in mtDNA depletion caused by long term treatment with ddC or other pyrimidine analogs.
Gene Name:
CMPK2
Uniprot ID:
Q5EBM0
Molecular weight:
44958.27
Reactions
Adenosine triphosphate + Cytidine monophosphate → ADP + CDPdetails
General function:
Involved in oxidation reduction
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.
Gene Name:
RRM1
Uniprot ID:
P23921
Molecular weight:
90069.375
Reactions
dCDP + Thioredoxin disulfide + Water → Thioredoxin + CDPdetails
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Inhibits Wnt signaling.
Gene Name:
RRM2
Uniprot ID:
P31350
Molecular weight:
44877.25
Reactions
dCDP + Thioredoxin disulfide + Water → Thioredoxin + CDPdetails
General function:
Involved in 6-phosphofructokinase activity
Specific function:
Catalyzes the third step of glycolysis, the phosphorylation of fructose-6-phosphate (F6P) by ATP to generate fructose-1,6-bisphosphate (FBP) and ADP.
Gene Name:
PFKL
Uniprot ID:
P17858
Molecular weight:
85017.825
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate → CDP + D-Tagatose 1,6-bisphosphatedetails
General function:
Involved in 6-phosphofructokinase activity
Specific function:
Catalyzes the third step of glycolysis, the phosphorylation of fructose-6-phosphate (F6P) by ATP to generate fructose-1,6-bisphosphate (FBP) and ADP.
Gene Name:
PFKM
Uniprot ID:
P08237
Molecular weight:
85181.925
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate → CDP + D-Tagatose 1,6-bisphosphatedetails
General function:
Involved in 6-phosphofructokinase activity
Specific function:
Catalyzes the third step of glycolysis, the phosphorylation of fructose-6-phosphate (F6P) by ATP to generate fructose-1,6-bisphosphate (FBP) and ADP.
Gene Name:
PFKP
Uniprot ID:
Q01813
Molecular weight:
85595.405
Reactions
Cytidine triphosphate + D-Tagatose 6-phosphate → CDP + D-Tagatose 1,6-bisphosphatedetails

Only showing the first 10 proteins. There are 32 proteins in total.