Modification Summary

5-hydroxymethylcytidine

[show modification pathway]
hm5C

Summary

Full name5-hydroxymethylcytidine
Short namehm5C
New Nomenclature51C
RNAMods abbreviation
HTML abbreviation
Enzymes
Found in phylogeny
Found in RNA
SMILES codeC3(OC(CO)C(O)C(O)3)N1C=C(CO)C(N)=NC1(=O)

LC-MS Information

Sum formulaC10O6N3H15
Monoisotopic mass273.0961
Average mass273.246
[M+H]+274.1039
Product ions142
Normalized LC elution time *0,52 (Kellner 2014)
LC elution order/characteristicsbetween C and U (Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Download [.mol file for hm5C]

Chemical groups contained

otherhydroxymethyl

Reactions producing 5-hydroxymethylcytidine

Name
C:hm5C

Occurrence in PDB structures

PDB-ID chain residue
1ve8 A 5FC /9
1ve8 B 5FC /9

Last modification of this entry: 2017-10-06 15:55:47.610775
Edited by a user: pboccaletto
Edited content: Changed mass_prot.