1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one

• ChemBase ID: 2771
• Molecular Formular: C9H12N2O5
• Molecular Mass: 228.20198
• Monoisotopic Mass: 228.07462149
• SMILES: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cccnc1=O
• Canonical SMILES: OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cccnc1=O
• 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
• InChIKey: RPQZTTQVRYEKCR-WCTZXXKLSA-N

NAMES AND DATABASE IDS

Names

• IUPAC name: 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
• IUPAC Traditional name: zebularine
• Synonyms: 1-(β-D-Ribofuranosyl)-1,2-dihydropyrimidin-2-one; 2-Pyrimidone-1-β-D-riboside; Zebularine; pyrimidin-2-one beta-ribofuranoside; Pyrimidin-2-one ribonucleoside; Pyrimidin-2-one beta-D-ribofuranoside; 1-beta-D-ribofuranosyl-2(1H)-pyrimidinone; 1-beta-D-ribofuranosylpyrimidin-2(1H)-one; DHZ; Zebularine; Pyrimidin-2-one β-D-ribofuranoside

Database IDs

• CAS Number: 3690-10-6
• MDL Number: MFCD04973699
• PubChem SID: 160966219; 46504541
• PubChem CID: 100016
• Chemspider ID: 90372
• Wikipedia Title: Zebularine

CALCULATED PROPERTIES

JChem

• Acid pKa: 12.553243
• H Acceptors: 6
• H Donor: 3
• LogD (pH = 5.5): -2.2063577
• LogD (pH = 7.4): -2.2063606
• Log P: -2.2063575
• Molar Refractivity: 51.6751 cm^3
• Polarizability: 20.316578 Å^3
• Polar Surface Area: 102.59 Å^2
• Rotatable Bonds: 2
• Lipinski's Rule of Five: true

ALOGPS 2.1

• Log P: -1.3
• LOG S: -0.59
• Solubility (Water): 5.82e+01 g/l

PROPERTIES

Physical Property

• Solubility: DMSO: soluble16 mg/mL
• Apperance: solid

Safety Information

• German water hazard class: 3
• Personal Protective Equipment: Eyeshields, Gloves, type N95 (US), type P1 (EN143) respirator filter
• Storage Temperature: 2-8°C

Product Information

• Purity: ≥98% (HPLC)
• Empirical Formula (Hill Notation): C9H12N2O5

DETAILS

DrugBank - DB03068

• Drug 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.

Sigma Aldrich - Z4775

Biochem/physiol Actions
Zebularine is a cytidine analogue, cytidine deaminase inhibitor, and DNA demethylating agent.