m5dC – 5-methyl-2'-deoxycytidine

Name
WID m5dC View in model
Name 5-methyl-2'-deoxycytidine View in model
Traditional name 4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidin-2-one
IUPAC name 4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2-dihydropyrimidin-2-one
Cross references PubChem: 6383, CAS: 838-07-3, KEGG: C03592
 
Classification
Type modified_deoxyribonucleoside_methylation View in model
 
Structure
Empirical formula (pH 7.5) H15C10N3O4
SMILES (pH 7.5) CC1=CN(C(=O)N=C1N)C2CC(C(O2)CO)O
Charge (pH 7.5) 0
Is hydrophobic False View in model
Molecular weight (Da) 241.24 View in model
van der Waals volume 
(pH 7.5; Å3 molecule‑1)
209.35
ΔfG'o (pH 7.5, 25C, I = 0; kJ mol‑1) 307.90
pI 7.82
logP -1.50
logD (pH 7.5) -1.50
 
Concentrations
Media composition (SP4; mM) 0.000207 View in model
 
Function
Reaction participant View in model
 
Comments
Comments occurs in bacteriophage DNA [PUB_0477]; 100% cytidine replacement in phage XP12 [PUB_0478]; 0.3-2% cytidine replacement in bacteria [PUB_0478];
References
  1. Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. FASEB J 9, 1034-42 (1995). WholeCell: PUB_0478, PubMed: 7649402

  2. Warren RA. Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34, 137-58 (1980). WholeCell: PUB_0477, PubMed: 7002022

 
Metadata
Created 2012-10-01 15:07:02
Last updated 2012-10-01 15:12:20