5-chloro-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione

• ChemBase ID: 109483
• Molecular Formular: C9H11ClN2O5
• Molecular Mass: 262.64704
• Monoisotopic Mass: 262.03564914
• SMILES: OC[C@H]1O[C@H](C[C@@H]1O)n1cc(Cl)c(=O)[nH]c1=O
• Canonical SMILES: OC[C@H]1O[C@H](C[C@@H]1O)n1cc(Cl)c(=O)[nH]c1=O
• InChI: InChI=1S/C9H11ClN2O5/c10-4-2-12(9(16)11-8(4)15)7-1-5(14)6(3-13)17-7/h2,5-7,13-14H,1,3H2,(H,11,15,16)/t5-,6+,7+/m0/s1
• InChIKey: NJCXGFKPQSFZIB-RRKCRQDMSA-N

NAMES AND DATABASE IDS

Names

• IUPAC name: 5-chloro-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
• IUPAC Traditional name: 5-chloro-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-pyrimidine-2,4-dione
• Synonyms: 5-CHLORODESOXYURIDINE; CldU; 5-Chloro-2′-deoxyuridine

Database IDs

• CAS Number: 50-90-8
• MDL Number: MFCD00006531
• PubChem SID: 24892910; 162095245
• PubChem CID: 65510

CALCULATED PROPERTIES

• Acid pKa: 7.972004
• H Acceptors: 5
• H Donor: 3
• LogD (pH = 5.5): -0.85526407
• LogD (pH = 7.4): -0.95558345
• Log P: -0.8538184
• Molar Refractivity: 55.8462 cm^3
• Polarizability: 22.147081 Å^3
• Polar Surface Area: 99.1 Å^2
• Rotatable Bonds: 2
• Lipinski's Rule of Five: true

PROPERTIES

Safety Information

• RTECS: YU7400000
• European Hazard Symbols: Harmful (Xn)
• German water hazard class: 3
• Risk Statements: 20/21/22-40
• Safety Statements: 36/37/39-45
• GHS Pictograms: GHS07; GHS08
• GHS Signal Word: Warning
• GHS Hazard statements: H302-H312-H332-H351
• GHS Precautionary statements: P280
• Personal Protective Equipment: dust mask type N95 (US), Eyeshields, Gloves
• Storage Temperature: -20°C

DETAILS

MP Biomedicals - 05211230

MP Biomedicals Rare Chemical collection

Sigma Aldrich - C6891

Application
5-Chloro-2′-deoxyuridine (CldU) is used as a thymidine analogue to study the miscoding potential of hypochlorous acid damage to DNA and DNA precursors. When used with antibody based immunofluorescent imaging, 5-Chloro-2′-deoxyuridine incorporation may be used in protocols to identify sites of DNA replication. CldU may be used as a labeling substrate in conjunction with other halogenated uridine labeling substrates such as bromodeoxyuridine (BrdU) and/or iododeoxyuridine (IdU).