Zebularine

Identification

Generic Name
Zebularine
DrugBank Accession Number
DB03068
Background

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

Type
Small Molecule
Groups
Experimental
Structure
Thumb
Weight
Average: 228.202
Monoisotopic: 228.074621504
Chemical Formula
C9H12N2O5
Synonyms
  • 1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
  • 1-beta-D-ribofuranosylpyrimidin-2(1H)-one
  • 4-deoxyuridine
  • Pyrimidin-2-one beta-D-ribofuranoside
  • pyrimidin-2-one beta-ribofuranoside
  • Pyrimidin-2-one ribonucleoside
External IDs
  • NSC-309132

Pharmacology

Indication

Not Available

Pharmacology
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Contraindications & Blackbox Warnings
Contraindications
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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

Adverse Effects
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Toxicity

Not Available

Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Not Available
Food Interactions
Not Available

Categories

Drug Categories
Chemical TaxonomyProvided by Classyfire
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
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Substituents
Alcohol / Aromatic heteromonocyclic compound / Azacycle / Glycosyl compound / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Monosaccharide / N-glycosyl compound / Organic nitrogen compound
show 14 more
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
pyrimidine ribonucleosides (CHEBI:46938)
Affected organisms
Not Available

Chemical Identifiers

UNII
7A9Y5SX0GY
CAS number
3690-10-6
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
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC=NC1=O

References

General References
Not Available
PubChem Compound
100016
PubChem Substance
46504541
ChemSpider
90372
BindingDB
50226311
ChEBI
46938
ChEMBL
CHEMBL504567
ZINC
ZINC000006119090
PDBe Ligand
ZE8
Wikipedia
Zebularine
PDB Entries
4pd7
MSDS
Download (24.1 KB)

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

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

Targets

Drugtargets
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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. [Article]
  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. [Article]

Drug created on June 13, 2005 13:24 / Updated on June 12, 2020 16:52