m5dC – 5-methyl-2'-deoxycytidine

Name
WID	m5dC
Name	5-methyl-2'-deoxycytidine
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

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
Molecular weight (Da)	241.24
van der Waals volume (pH 7.5; Å³ molecule^‑1)	209.35
Δ_fG^'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

Function
Reaction participant	5-methyl-2'-deoxycytidine transport m5dC[e] ⇔ m5dC[c] 5'-nucleotidase (5-methyl-2'-deoxycytidine monophosphate) [c]: H2O + m5dCMP ⇒ m5dC + PI

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	Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. FASEB J 9, 1034-42 (1995). WholeCell: PUB_0478, PubMed: 7649402 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