Record Information
Version 1.0
Update Date 1/22/2018 12:54:53 PM
Metabolite IDPAMDB000415
Identification
Name: CDP
Description:Cytidine 5'-(trihydrogen diphosphate) is cytosine nucleotide containing two phosphate groups esterified to the sugar (ribose) moiety.
Structure
Thumb
Synonyms:
  • CDP
  • Cytidine-5'-diphosphate
  • Cytidine-5'-diphosphoric acid
  • Cytidine-diphosphate
  • Cytidine-diphosphoric acid
Chemical Formula: C9H15N3O11P2
Average Molecular Weight: 403.1764
Monoisotopic Molecular Weight: 403.018181361
InChI Key: ZWIADYZPOWUWEW-XVFCMESISA-N
InChI: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
CAS number: 63-38-7
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: CDP
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
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside diphosphate
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Pyrimidone
  • Aminopyrimidine
  • Imidolactam
  • Alkyl phosphate
  • Pyrimidine
  • Primary aromatic amine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Saccharide
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:2.44 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility10.1 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity76.29 m3·mol-1ChemAxon
Polarizability31.39 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
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 Available
1D NMR13C NMR SpectrumNot Available
References
References:
  • 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
  • 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
  • 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
  • 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
  • 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
  • Ishii, N., Nakahigashi, K., Baba, T., Robert, M., Soga, T., Kanai, A., Hirasawa, T., Naba, M., Hirai, K., Hoque, A., Ho, P. Y., Kakazu, Y., Sugawara, K., Igarashi, S., Harada, S., Masuda, T., Sugiyama, N., Togashi, T., Hasegawa, M., Takai, Y., Yugi, K., Arakawa, K., Iwata, N., Toya, Y., Nakayama, Y., Nishioka, T., Shimizu, K., Mori, H., Tomita, M. (2007). "Multiple high-throughput analyses monitor the response of E. coli to perturbations." Science 316:593-597. Pubmed: 17379776
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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
  • Nowicki M, Muller F, Frentzen M: Cardiolipin synthase of Arabidopsis thaliana. FEBS Lett. 2005 Apr 11;579(10):2161-5. Pubmed: 15811335
  • 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
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Chambers, 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
External Links:
ResourceLink
CHEBI ID17239
HMDB IDHMDB01546
Pubchem Compound ID6132
Kegg IDC00112
ChemSpider ID5902
WikipediaCDP
BioCyc IDCDP
EcoCyc IDCDP
Ligand ExpoCDP

Enzymes

General function:
Involved in oxidation-reduction process
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines
Gene Name:
nrdA
Locus Tag:
PA1156
Molecular weight:
107.1 kDa
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in RNA binding
Specific function:
Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3'- to 5'-direction
Gene Name:
pnp
Locus Tag:
PA4740
Molecular weight:
75.4 kDa
Reactions
RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
General function:
Involved in cytidylate kinase activity
Specific function:
ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors
Gene Name:
cmk
Locus Tag:
PA3163
Molecular weight:
24.6 kDa
Reactions
ATP + (d)CMP = ADP + (d)CDP.
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
Gene Name:
ndk
Locus Tag:
PA3807
Molecular weight:
15.6 kDa
Reactions
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
General function:
Involved in ATP binding
Specific function:
Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth
Gene Name:
adk
Locus Tag:
PA3686
Molecular weight:
23.1 kDa
Reactions
ATP + AMP = 2 ADP.
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R2 contains the tyrosyl radical required for catalysis
Gene Name:
nrdB
Locus Tag:
PA1155
Molecular weight:
47.4 kDa
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin.
General function:
Involved in electron carrier activity
Specific function:
Monothiol glutaredoxin involved in the biogenesis of iron-sulfur clusters (Probable)
Gene Name:
grxD
Locus Tag:
PA3533
Molecular weight:
11.8 kDa
General function:
Involved in electron carrier activity
Specific function:
The disulfide bond functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. In addition, it is also involved in reducing some disulfides in a coupled system with glutathione reductase
Gene Name:
grxC
Locus Tag:
PA5129
Molecular weight:
9.2 kDa
General function:
Involved in electron carrier activity
Specific function:
Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions
Gene Name:
trxA
Locus Tag:
PA5240
Molecular weight:
11.9 kDa