Zebularine

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

Status : 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.

Chemical Classification

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.

Pyrimidine nucleosides

Organic compounds

Nucleosides, nucleotides, and analogues

Pyrimidine nucleosides

Chemical Name

1-beta-D-ribofuranosyl-2(1H)-pyrimidinone

Calculated Property

kind Value Source
logP -1.3 ALOGPS
logS -0.59 ALOGPS
Water Solubility 5.82e+01 g/l ALOGPS
logP -2.2 ChemAxon
IUPAC Name 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one ChemAxon
Traditional IUPAC Name zebularine ChemAxon
Molecular Weight 228.202 ChemAxon
Monoisotopic Weight 228.074621504 ChemAxon
SMILES OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC=NC1=O ChemAxon
Molecular Formula C9H12N2O5 ChemAxon
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 ChemAxon
InChIKey InChIKey=RPQZTTQVRYEKCR-WCTZXXKLSA-N ChemAxon
Polar Surface Area (PSA) 102.59 ChemAxon
Refractivity 51.68 ChemAxon
Polarizability 20.83 ChemAxon
Rotatable Bond Count 2 ChemAxon
H Bond Acceptor Count 6 ChemAxon
H Bond Donor Count 3 ChemAxon
pKa (strongest acidic) 12.55 ChemAxon
pKa (strongest basic) -3 ChemAxon
Physiological Charge 0 ChemAxon
Number of Rings 2 ChemAxon
Bioavailability 1 ChemAxon
Rule of Five 1 ChemAxon
Ghose Filter 0 ChemAxon
MDDR-Like Rule 0 ChemAxon

Target within organism

  • Cytidine deaminase : in Escherichia coli (strain K12)