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CDP (YMDB00064)

Identification
YMDB IDYMDB00064
NameCDP
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
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
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • CDP
  • cytidine-5'-diphosphate
  • cytidine-diphosphate
  • 5'-CDP
  • Cytidine 5'-diphosphate
  • Cytidine 5'-diphosphoric acid
  • Cytidine 5'-pyrophosphate
  • Cytidine diphosphate
  • Cytidine, 5'-(trihydrogen pyrophosphate)
  • Cytidine 5'-pyrophosphoric acid
  • Cytidine diphosphoric acid
  • Cytidine, 5'-(trihydrogen pyrophosphoric acid)
  • CYTIDINE-5'-diphosphoric acid
  • Diphosphate, cytidine
CAS number63-38-7
WeightAverage: 403.1764
Monoisotopic: 403.018181361
InChI KeyZWIADYZPOWUWEW-XVFCMESISA-N
InChIInChI=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
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 NameCDP
Chemical FormulaC9H15N3O11P2
SMILES[H]O[C@]1([H])[C@]([H])(O[H])[C@]([H])(O[C@@]1([H])N1C([H])=C([H])C(=NC1=O)N([H])[H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H]
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
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogP2.44 [HANSCH,C ET AL. (1995)]PhysProp
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
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • nucleus
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Choline metabolismPW002494 ThumbThumb?image type=greyscaleThumb?image type=simple
Glycerophospholipid metabolismPW002493 ThumbThumb?image type=greyscaleThumb?image type=simple
N-Glycan biosynthesisPW002501 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
Triacylglycerol metabolismPW002695 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Glycerophospholipid metabolismec00564 Map00564
N-Glycan biosynthesisec00510 Map00510
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
CDP + reduced thioredoxin → water + oxidized thioredoxin + dCDP
CDP + a reduced NrdH glutaredoxin-like protein → water + dCDP + an oxidized NrdH glutaredoxin-like protein
DG(16:0/16:0/0:0) + Cytidine triphosphate → PA(16:0/16:0) + hydron + CDP
DG(10:0/10:0/0:0) + Cytidine triphosphate → PA(10:0/10:0) + hydron + CDP
DG(10:0/12:0/0:0) + Cytidine triphosphate → PA(10:0/12:0) + hydron + CDP
KEGG Reactions
Adenosine triphosphate + Cytidine monophosphate ↔ CDP + ADP
Dolichol-20 + Cytidine triphosphate → dolichyl phosphate + CDP + hydron
(R)-Mevalonic acid + Cytidine triphosphate → Mevalonic acid-5P + CDP + hydron
Adenosine triphosphate + CDP ↔ ADP + Cytidine triphosphate
thioredoxin dithiol + CDP → dCDP + thioredoxin disulfide + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-5923000000-f7e7b227d8dab9e29e4bJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-00di-3209010000-ff27ee45250db3e35193JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-004i-9000000000-f5d958a3ccf576052a6bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-00di-0390000000-0274cdf4190792442001JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , negativesplash10-0udi-0009000000-2c8a9272dc29076a6167JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-0kdi-9602700000-4b46ddc9506634a02dc5JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-0a4i-0059000000-d598d99a604dda402181JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0udi-0003900000-69398917fb0c37a4304fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-0zg0-0726900000-8d967e8ca6677a467fb8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0k9i-0927400000-86e5ba01091f928ca88fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0kdi-9814400000-54042f12a186a46a5a17JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Positivesplash10-0k9i-0927400000-61338365caaf6cc96eddJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-03di-0900000000-2e5da7181d5154fd5287JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-8913200000-d327869c80aa6b6ba8b7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-7913200000-4f2656e2010a4274c652JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-ae7cefa275aa112f8ff3JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0000900000-1f74a916c1bec3408d2eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-056r-9601000000-0261d005e8d3964fc255JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 30V, Negativesplash10-056r-8913200000-3093e23d54c628f19ea0JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0901000000-6aed044cc4135aa261dfJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-3900000000-92fac6a8baf47bac3014JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-5900000000-5ad7bca4dc732a0e3840JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0903300000-44d24cfda26f8f0a8d96JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9701000000-d96a23308bcfcf9cf55fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-d7e0d2a5e8d20180b483JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0100900000-fd8a10c051d8566d4abcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9418200000-cd847d00773e220445ddJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
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.
External Links:
ResourceLink
CHEBI ID17239
HMDB IDHMDB01546
Pubchem Compound ID6132
Kegg IDC00112
ChemSpider ID5902
FOODB IDFDB022683
WikipediaCDP
BioCyc IDCDP

Enzymes

Protein Details
1. Dolichol kinase
General function:
Involved in transferase activity, transferring phosphorus-containing groups
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. It is required for spore germination. Has an essential role in cellular metabolism
Gene Name:
SEC59
Uniprot ID:
P20048
Molecular weight:
58905.39844
Reactions
CTP + dolichol → CDP + dolichyl phosphate.
Protein Details
2. CTP-dependent diacylglycerol kinase 1
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Involved in pre-tRNA splicing. CTP- dependent diacylglycerol kinase that catalyzes the phosphorylation of diacylglycerol (DAG) to phosphatidate (PA). Controls phosphatidate levels at the nuclear envelope. Counteracts the activity of PAH1/SMP2. Involved in the resistance to nickel chloride and nalidixic acid. May be involved in vesicle trafficking between the endoplasmic reticulum and the Golgi apparatus
Gene Name:
DGK1
Uniprot ID:
Q12382
Molecular weight:
32839.80078
Reactions
CTP + 1,2-diacyl-sn-glycerol → CDP + 1,2-diacyl-sn-glycerol 3-phosphate.
Protein Details
3. Ribonucleoside-diphosphate reductase small chain 1
General function:
Involved in oxidoreductase activity
Specific function:
Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
Gene Name:
RNR2
Uniprot ID:
P09938
Molecular weight:
46147.0
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
Protein Details
4. Nucleoside diphosphate kinase
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. Required for repair of UV radiation- and etoposide-induced DNA damage
Gene Name:
YNK1
Uniprot ID:
P36010
Molecular weight:
17166.59961
Reactions
ATP + nucleoside diphosphate → ADP + nucleoside triphosphate.
Protein Details
5. Ribonucleoside-diphosphate reductase large chain 1
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
Gene Name:
RNR1
Uniprot ID:
P21524
Molecular weight:
99560.20313
Reactions
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin.
Protein Details
6. Mevalonate kinase
General function:
Involved in ATP binding
Specific function:
RAR (regulation of autonomous replication) is a protein whose activity increases the mitotic stability of plasmids
Gene Name:
ERG12
Uniprot ID:
P07277
Molecular weight:
48458.89844
Reactions
ATP + (R)-mevalonate → ADP + (R)-5-phosphomevalonate.