Identification
NameCytidine-5'-Diphosphate
Accession NumberDB04555  (EXPT00868)
TypeSmall Molecule
GroupsExperimental
Description

Cytidine 5'-(trihydrogen diphosphate). A cytosine nucleotide containing two phosphate groups esterified to the sugar moiety. Synonyms: CRPP; cytidine pyrophosphate. [PubChem]

Structure
Thumb
SynonymsNot Available
External IDs Not Available
Product Ingredients Not Available
Approved Prescription ProductsNot Available
Approved Generic Prescription ProductsNot Available
Approved Over the Counter ProductsNot Available
Unapproved/Other Products Not Available
International BrandsNot Available
Brand mixturesNot Available
CategoriesNot Available
UNII1ZH821MXU5
CAS number63-38-7
WeightAverage: 403.1764
Monoisotopic: 403.018181361
Chemical FormulaC9H15N3O11P2
InChI KeyZWIADYZPOWUWEW-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
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
SMILES
NC1=NC(=O)N(C=C1)[C@@H]1O[[email protected]](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[[email protected]]1O
Pharmacology
IndicationNot Available
Structured Indications Not Available
PharmacodynamicsNot Available
Mechanism of action
TargetKindPharmacological actionActionsOrganismUniProt ID
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseProteinunknownNot AvailableShigella flexneriP62619 details
3-deoxy-manno-octulosonate cytidylyltransferaseProteinunknownNot AvailableEscherichia coliP42216 details
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseProteinunknownNot AvailableThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Q8RQP5 details
N-acylneuraminate cytidylyltransferaseProteinunknownNot AvailableNeisseria meningitidisP0A0Z8 details
Cytidylate kinaseProteinunknownNot AvailableEscherichia coli (strain K12)P0A6I0 details
CDP-paratose 2-epimeraseProteinunknownNot AvailableSalmonella typhiP14169 details
Related Articles
AbsorptionNot Available
Volume of distributionNot Available
Protein bindingNot Available
MetabolismNot Available
Route of eliminationNot Available
Half lifeNot Available
ClearanceNot Available
ToxicityNot Available
Affected organismsNot Available
PathwaysNot Available
Pharmacogenomic Effects/ADRs Not Available
Interactions
Drug Interactions Not Available
Food InteractionsNot Available
References
Synthesis ReferenceNot Available
General ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Clinical Trials
Clinical Trials Not Available
Pharmacoeconomics
ManufacturersNot Available
PackagersNot Available
Dosage formsNot Available
PricesNot Available
PatentsNot Available
Properties
StateSolid
Experimental PropertiesNot Available
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 FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption-0.8988
Blood Brain Barrier+0.9126
Caco-2 permeable-0.7763
P-glycoprotein substrateNon-substrate0.7622
P-glycoprotein inhibitor INon-inhibitor0.9175
P-glycoprotein inhibitor IINon-inhibitor0.9806
Renal organic cation transporterNon-inhibitor0.96
CYP450 2C9 substrateNon-substrate0.7402
CYP450 2D6 substrateNon-substrate0.8462
CYP450 3A4 substrateNon-substrate0.596
CYP450 1A2 substrateNon-inhibitor0.9167
CYP450 2C9 inhibitorNon-inhibitor0.9233
CYP450 2D6 inhibitorNon-inhibitor0.9134
CYP450 2C19 inhibitorNon-inhibitor0.9043
CYP450 3A4 inhibitorNon-inhibitor0.9438
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.974
Ames testNon AMES toxic0.9125
CarcinogenicityNon-carcinogens0.9062
BiodegradationNot ready biodegradable0.7826
Rat acute toxicity2.2404 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9834
hERG inhibition (predictor II)Non-inhibitor0.8137
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397 )
Spectra
Mass Spec (NIST)Not Available
Spectra
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9000000000-f5d958a3ccf576052a6bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-00di-0390000000-0274cdf4190792442001View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , 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-APPI-QQ , 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 Available
1D NMR13C NMR SpectrumNot Available
Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct ParentPyrimidine ribonucleoside diphosphates
Alternative ParentsPentose phosphates / Glycosylamines / Organic pyrophosphates / Monosaccharide phosphates / Aminopyrimidines and derivatives / Pyrimidones / Monoalkyl phosphates / Primary aromatic amines / Hydropyrimidines / Imidolactams
SubstituentsPyrimidine ribonucleoside diphosphate / Pentose phosphate / Pentose-5-phosphate / Glycosyl compound / N-glycosyl compound / Monosaccharide phosphate / Organic pyrophosphate / Pentose monosaccharide / Aminopyrimidine / Pyrimidone
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptorscytidine 5'-phosphate, pyrimidine ribonucleoside 5'-diphosphate (CHEBI:17239 ) / Ribonucleotides (C00112 )

Targets

Kind
Protein
Organism
Shigella flexneri
Pharmacological action
unknown
General Function:
Metal ion binding
Specific Function:
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).
Gene Name:
ispF
Uniprot ID:
P62619
Molecular Weight:
16897.37 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Escherichia coli
Pharmacological action
unknown
General Function:
3-deoxy-manno-octulosonate cytidylyltransferase activity
Specific Function:
Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
Gene Name:
kpsU
Uniprot ID:
P42216
Molecular Weight:
27158.885 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Pharmacological action
unknown
General Function:
Metal ion binding
Specific Function:
Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP).
Gene Name:
ispF
Uniprot ID:
Q8RQP5
Molecular Weight:
16519.835 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Neisseria meningitidis
Pharmacological action
unknown
General Function:
N-acylneuraminate cytidylyltransferase activity
Specific Function:
Not Available
Gene Name:
neuA
Uniprot ID:
P0A0Z8
Molecular Weight:
24892.155 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
unknown
General Function:
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
Uniprot ID:
P0A6I0
Molecular Weight:
24746.03 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Kind
Protein
Organism
Salmonella typhi
Pharmacological action
unknown
General Function:
Cdp-abequose epimerase activity
Specific Function:
Catalyzes the isomeration of CDP-paratose to CDP-tyvelose.
Gene Name:
rfbE
Uniprot ID:
P14169
Molecular Weight:
37957.675 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
Drug created on June 13, 2005 07:24 / Updated on June 11, 2017 16:35