Modification Summary

3-methylcytidine

[show modification pathway]
m3C

Summary

Full name3-methylcytidine
Short namem3C
New Nomenclature3C
RNAMods abbreviation'
HTML abbreviation'
Enzymes Trm140 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota
Found in RNAtRNA
PubChem ID159649
SMILES codeC[N+]1=C(N)C=CN([C@@H]2O[C@H](CO)[C@H](O)C2O)C1=O

LC-MS Information

Sum formulaC10O5N3H15
Monoisotopic mass257.10117
Average mass257.2467
HRMS mass257.100621
Normalized LC elution time *0,55 (Kellner 2014); 0,54 (Kellner 2014)
LC elution order/characteristicsbetween C and U (Kellner 2014, Kellner 2014)
Mass transition-132 (Kellner 2014, Kellner 2014, Su 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
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -
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 m3C]

Comments

m3C has a positive charge at neutral pH.

Chemical groups contained

methyl groupmethyl at aromatic N

Reactions producing 3-methylcytidine

Name
C:m3C

Occurrence in PDB structures

PDB-ID chain residue
1b5k A EDC /6
1b60 A EDC /6
1b6x A EDC /6
1b6y A EDC /6
1n5c A EDC /21

Last modification of this entry: 2017-07-05 14:53:24.455168
Edited by a user: pboccaletto
Edited content: Changed lc_elution_time, lc_elution_comment, lc_reference and mass_trans.