You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on DrugBank.
Identification
NameZebularine
Accession NumberDB03068  (EXPT03280)
TypeSmall Molecule
GroupsExperimental
Description

A chemically stable, cytidine analog that displays anti-tumor properties. Acts as a transition state analog inhibitor of cytidine deaminase by binding to the active size as covalent hydrates. Also shown to inhibit DNA methylation and tumor growth both in vitro and in vivo.

Structure
Thumb
Synonyms
1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
1-beta-D-ribofuranosylpyrimidin-2(1H)-one
DHZ
Pyrimidin-2-one beta-D-ribofuranoside
pyrimidin-2-one beta-ribofuranoside
Pyrimidin-2-one ribonucleoside
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 number3690-10-6
WeightAverage: 228.202
Monoisotopic: 228.074621504
Chemical FormulaC9H12N2O5
InChI KeyInChIKey=RPQZTTQVRYEKCR-WCTZXXKLSA-N
InChI
InChI=1S/C9H12N2O5/c12-4-5-6(13)7(14)8(16-5)11-3-1-2-10-9(11)15/h1-3,5-8,12-14H,4H2/t5-,6-,7-,8-/m1/s1
IUPAC Name
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
SMILES
OC[[email protected]]1O[[email protected]]([[email protected]](O)[C@@H]1O)N1C=CC=NC1=O
Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Pyrimidone
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
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+0.8866
Blood Brain Barrier+0.7864
Caco-2 permeable-0.885
P-glycoprotein substrateNon-substrate0.814
P-glycoprotein inhibitor INon-inhibitor0.9398
P-glycoprotein inhibitor IINon-inhibitor0.9241
Renal organic cation transporterNon-inhibitor0.9304
CYP450 2C9 substrateNon-substrate0.7055
CYP450 2D6 substrateNon-substrate0.8617
CYP450 3A4 substrateNon-substrate0.5787
CYP450 1A2 substrateNon-inhibitor0.8999
CYP450 2C9 inhibitorNon-inhibitor0.9498
CYP450 2D6 inhibitorNon-inhibitor0.9357
CYP450 2C19 inhibitorNon-inhibitor0.9439
CYP450 3A4 inhibitorNon-inhibitor0.9654
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9525
Ames testNon AMES toxic0.7318
CarcinogenicityNon-carcinogens0.9282
BiodegradationReady biodegradable0.7594
Rat acute toxicity1.8260 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9751
hERG inhibition (predictor II)Non-inhibitor0.8781
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 Solubility58.2 mg/mLALOGPS
logP-1.3ALOGPS
logP-2.2ChemAxon
logS-0.59ALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area102.59 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity51.68 m3·mol-1ChemAxon
Polarizability20.83 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
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
MSDSDownload (24.1 KB)
Interactions
Drug InteractionsNot Available
Food InteractionsNot Available

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
unknown
General Function:
Zinc ion binding
Specific Function:
This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
Gene Name:
cdd
Uniprot ID:
P0ABF6
Molecular Weight:
31539.445 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 ]
Comments
comments powered by Disqus
Drug created on June 13, 2005 07:24 / Updated on September 16, 2013 17:20