Zebularine
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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
- 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
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- Pharmacodynamics
Not Available
- Mechanism of action
Target Actions Organism UCytidine deaminase Not Available Escherichia 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
- Improve decision support & research outcomesWith structured adverse effects data, including: blackbox warnings, adverse reactions, warning & precautions, & incidence rates. View sample adverse effects data in our new Data Library!Improve decision support & research outcomes with our structured adverse effects data.
- 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 show 4 more
- 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
- External Links
- 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
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
Property Value Source Water Solubility 58.2 mg/mL ALOGPS logP -1.3 ALOGPS logP -2.2 Chemaxon logS -0.59 ALOGPS pKa (Strongest Acidic) 12.55 Chemaxon pKa (Strongest Basic) 0.3 Chemaxon Physiological Charge 0 Chemaxon Hydrogen Acceptor Count 6 Chemaxon Hydrogen Donor Count 3 Chemaxon Polar Surface Area 102.59 Å2 Chemaxon Rotatable Bond Count 2 Chemaxon Refractivity 51.68 m3·mol-1 Chemaxon Polarizability 20.9 Å3 Chemaxon Number of Rings 2 Chemaxon Bioavailability 1 Chemaxon Rule of Five Yes Chemaxon Ghose Filter No Chemaxon Veber's Rule No Chemaxon MDDR-like Rule No Chemaxon - Predicted ADMET Features
Property Value Probability Human Intestinal Absorption + 0.8866 Blood Brain Barrier + 0.7864 Caco-2 permeable - 0.885 P-glycoprotein substrate Non-substrate 0.814 P-glycoprotein inhibitor I Non-inhibitor 0.9398 P-glycoprotein inhibitor II Non-inhibitor 0.9241 Renal organic cation transporter Non-inhibitor 0.9304 CYP450 2C9 substrate Non-substrate 0.7055 CYP450 2D6 substrate Non-substrate 0.8617 CYP450 3A4 substrate Non-substrate 0.5787 CYP450 1A2 substrate Non-inhibitor 0.8999 CYP450 2C9 inhibitor Non-inhibitor 0.9498 CYP450 2D6 inhibitor Non-inhibitor 0.9357 CYP450 2C19 inhibitor Non-inhibitor 0.9439 CYP450 3A4 inhibitor Non-inhibitor 0.9654 CYP450 inhibitory promiscuity Low CYP Inhibitory Promiscuity 0.9525 Ames test Non AMES toxic 0.7318 Carcinogenicity Non-carcinogens 0.9282 Biodegradation Ready biodegradable 0.7594 Rat acute toxicity 1.8260 LD50, mol/kg Not applicable hERG inhibition (predictor I) Weak inhibitor 0.9751 hERG inhibition (predictor II) Non-inhibitor 0.8781
Spectra
- Mass Spec (NIST)
- Not Available
- Spectra
Spectrum Spectrum Type Splash Key Predicted GC-MS Spectrum - GC-MS Predicted GC-MS splash10-0a6v-9510000000-ea2a38913e883670f506 Predicted MS/MS Spectrum - 10V, Positive (Annotated) Predicted LC-MS/MS splash10-00kb-9210000000-470513864d16c1f70499 Predicted MS/MS Spectrum - 10V, Negative (Annotated) Predicted LC-MS/MS splash10-0002-9110000000-23251ff8038519a4719e Predicted MS/MS Spectrum - 20V, Positive (Annotated) Predicted LC-MS/MS splash10-0007-9000000000-d8e56b2f313925f66911 Predicted MS/MS Spectrum - 20V, Negative (Annotated) Predicted LC-MS/MS splash10-0006-9000000000-09004aa4dbd1ec7b6cbe Predicted MS/MS Spectrum - 40V, Negative (Annotated) Predicted LC-MS/MS splash10-0006-9000000000-4d63eeca3a10584bd89b Predicted MS/MS Spectrum - 40V, Positive (Annotated) Predicted LC-MS/MS splash10-0002-9300000000-96ae14542e0f42b16143 Predicted 1H NMR Spectrum 1D NMR Not Applicable Predicted 13C NMR Spectrum 1D NMR Not Applicable - Chromatographic Properties
Collision Cross Sections (CCS)
Adduct CCS Value (Å2) Source type Source [M-H]- 148.68936 predictedDeepCCS 1.0 (2019) [M+H]+ 151.0854 predictedDeepCCS 1.0 (2019) [M+Na]+ 156.99794 predictedDeepCCS 1.0 (2019)
Targets
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1. DetailsCytidine deaminase
- 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
Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52