Zebularine

Identification

Name
Zebularine
Accession Number
DB03068  (EXPT03280)
Type
Small Molecule
Groups
Experimental
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 IDs
NSC-309132
Categories
UNII
7A9Y5SX0GY
CAS number
3690-10-6
Weight
Average: 228.202
Monoisotopic: 228.074621504
Chemical Formula
C9H12N2O5
InChI Key
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

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UCytidine deaminaseNot AvailableEscherichia coli (strain K12)
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
Not Available
Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
PubChem Compound
100016
PubChem Substance
46504541
ChemSpider
90372
ChEBI
46938
ChEMBL
CHEMBL504567
HET
ZE8
PDB Entries
4pd7
MSDS
Download (24.1 KB)

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not 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 FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
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)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSNot Available
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSNot Available

Taxonomy

Description
This 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.
Kingdom
Organic compounds
Super Class
Nucleosides, nucleotides, and analogues
Class
Pyrimidine nucleosides
Sub Class
Not Available
Direct Parent
Pyrimidine nucleosides
Alternative Parents
Glycosylamines / Pentoses / Pyrimidones / Hydropyrimidines / Tetrahydrofurans / Heteroaromatic compounds / Secondary alcohols / Oxacyclic compounds / Azacyclic compounds / Primary alcohols
show 4 more
Substituents
Pyrimidine nucleoside / Glycosyl compound / N-glycosyl compound / Pentose monosaccharide / Pyrimidone / Hydropyrimidine / Monosaccharide / Pyrimidine / Heteroaromatic compound / Tetrahydrofuran
show 14 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine ribonucleosides (CHEBI:46938)

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
Uniprot Name
Cytidine deaminase
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]

Drug created on June 13, 2005 07:24 / Updated on December 01, 2017 15:07