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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 Identifiers 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
SaltsNot Available
CategoriesNot Available
UNIINot Available
CAS number63-38-7
WeightAverage: 403.1764
Monoisotopic: 403.018181361
Chemical FormulaC9H15N3O11P2
InChI KeyInChIKey=ZWIADYZPOWUWEW-ZAKLUEHWSA-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+/m0/s1
IUPAC Name
[({[(2S,3R,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[C@@H](CO[P@](O)(=O)OP(O)(O)=O)[[email protected]](O)[[email protected]]1O
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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine 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 FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Pharmacology
IndicationNot Available
PharmacodynamicsNot Available
Mechanism of actionNot Available
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
SNP Mediated EffectsNot Available
SNP Mediated Adverse Drug ReactionsNot Available
ADMET
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 )
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
Polarizability31.6 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Mass Spec (NIST)Not Available
SpectraNot Available
References
Synthesis ReferenceNot Available
General ReferencesNot Available
External Links
ATC CodesNot Available
AHFS CodesNot Available
PDB Entries
FDA labelNot Available
MSDSNot Available
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

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 ]
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Drug created on June 13, 2005 07:24 / Updated on September 16, 2013 17:25