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

• ChemBase ID: 155788
• Molecular Formular: C9H12IN3O4
• Molecular Mass: 353.11375
• Monoisotopic Mass: 352.98725388
• SMILES: c1c(c(nc(=O)n1[C@H]1CC(C(O1)CO)O)N)I
• Canonical SMILES: OCC1O[C@H](CC1O)n1cc(I)c(nc1=O)N
• InChI: InChI=1S/C9H12IN3O4/c10-4-2-13(9(16)12-8(4)11)7-1-5(15)6(3-14)17-7/h2,5-7,14-15H,1,3H2,(H2,11,12,16)/t5?,6?,7-/m1/s1
• InChIKey: WEVJJMPVVFNAHZ-KPGICGJXSA-N

NAMES AND DATABASE IDS

Names

• IUPAC name: 4-amino-1-[(2R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-iodo-1,2-dihydropyrimidin-2-one
• IUPAC Traditional name: 4-amino-1-[(2R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-iodopyrimidin-2-one
• Synonyms: 5-Iododeoxycytidine; 5-Iodo-2′-deoxycytidine

Database IDs

• CAS Number: 611-53-0
• EC Number: 210-269-8
• MDL Number: MFCD00038063
• PubChem SID: 24896100; 162249926
• PubChem CID: 16219524

CALCULATED PROPERTIES

• Acid pKa: 13.894901
• H Acceptors: 6
• H Donor: 3
• LogD (pH = 5.5): -0.9111938
• LogD (pH = 7.4): -0.9111939
• Log P: -0.9111938
• Molar Refractivity: 66.3831 cm^3
• Polarizability: 26.099108 Å^3
• Polar Surface Area: 108.38 Å^2
• Rotatable Bonds: 2
• Lipinski's Rule of Five: true

PROPERTIES

Safety Information

• European Hazard Symbols: Harmful (Xn)
• German water hazard class: 3
• Risk Statements: 22
• GHS Pictograms: GHS07
• GHS Signal Word: Warning
• GHS Hazard statements: H302
• Personal Protective Equipment: dust mask type N95 (US), Eyeshields, Gloves
• Storage Temperature: -20°C

Product Information

• Purity: ≥99% (HPLC)
• Empirical Formula (Hill Notation): C9H12IN3O4

DETAILS

Sigma Aldrich - I7000

Application
5-Iodo-2′-deoxycytidine (5-iododeoxycytidine) is used in the construction of DNA oligomers to enable structural studies and photoactivated cross-linking. 5-Iodo-2′-deoxycytidine is used in the synthesis of other modified nucleosides, such as 5-ethynylferrocenyl-2′-deoxycytidine used in semiconductor electrodes and 10-(2-deoxyβ-D-ribofuranosyl)pyrimido[4′,5′:4,5]pyrimido[1,6-a]indole-6,9(7H)-dione (dCPPI).