4-amino-1-[(2R,4R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one

• ChemBase ID: 170790
• Molecular Formular: C10H15N3O5
• Molecular Mass: 257.2432
• Monoisotopic Mass: 257.1011706
• SMILES: [C@H]1(C[C@@H](O[C@@H]1CO)n1c(=O)nc(c(c1)CO)N)O
• Canonical SMILES: OC[C@H]1O[C@H](C[C@H]1O)n1cc(CO)c(nc1=O)N
• InChI: InChI=1S/C10H15N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h2,6-8,14-16H,1,3-4H2,(H2,11,12,17)/t6-,7-,8-/m1/s1
• InChIKey: HMUOMFLFUUHUPE-BWZBUEFSSA-N

NAMES AND DATABASE IDS

Names

• IUPAC name: 4-amino-1-[(2R,4R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one
• IUPAC Traditional name: 4-amino-1-[(2R,4R,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
• Synonyms: 2'-deoxy-5-(hydroxymethyl)cytidine; 5-(Hydroxymethyl)deoxycytidine; 5-(Hydroxymethyl)-2'-deoxycytidine

Database IDs

• CAS Number: 7226-77-9
• PubChem SID: 164226700
• PubChem CID: 71749131

CALCULATED PROPERTIES

• Acid pKa: 13.860356
• H Acceptors: 7
• H Donor: 4
• LogD (pH = 5.5): -2.7821
• LogD (pH = 7.4): -2.7821
• Log P: -2.7821
• Molar Refractivity: 59.1659 cm^3
• Polarizability: 23.29661 Å^3
• Polar Surface Area: 128.61 Å^2
• Rotatable Bonds: 3
• Lipinski's Rule of Five: true

DETAILS

Toronto Research Chemicals - H946630

4-(Hydroxymethyl)-2’-deoxycytidine is a modified pyrimidine that is capable of producing interstrand cross-links in duplex DNA. 4-(Hydroxymethyl)-2’-deoxycytidine can be analyzed to quantify DNA hydroxymethylation levels in biological samples

REFERENCES

• Peng, X. et al.: J. Am. Chem. Soc., 130, 10299 (2008)
• Berkner, K. et al.: J. Biol. Chem., 252, 3185 (2008)
• Le, T. et al.: Anal. Biochem., 412, 203 (2008)