Modomics - A Database of RNA Modifications

The molecule is shown in a ball-and-stick representation with the following colors for atoms :
Hydrogen (H): white Carbon (C): gray Oxygen (O): red Phosphorus (P): orange Nitrogen (N): blue Selenium (Se): gold Sulfur (S): yellow


Full name3-methylcytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-methylpyrimidin-1-ium-2-one
Short namem3C
MODOMICS code new2000000003C
Nature of the modified residueNatural
RNAMods code'
Residue unique ID52
Found in RNAYes
Related nucleotides299
Enzymes Trm140 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC10H16N3O5+
Type of moietynucleoside
Degeneracynot applicable
PubChem ID159649
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand AR3
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)

Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb


Tautomers SMILES
C[NH+]1C(=N)C=CN(C2OC(CO)C(O)C2O)C1=O tautomer #0
C[n+]1c(N)ccn(C2OC(CO)C(O)C2O)c1=O tautomer #1
C[n+]1c(=N)ccn(C2OC(CO)C(O)C2O)c1O tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

m3C m3C m3C

* CYP Metabolic sites predicted with SMARTCyp. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. The three top-ranked atoms are highlighted. See: SmartCYP and SmartCYP - background; Patrik Rydberg, David E. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 (link)

LC-MS Information

Monoisotopic mass257.1012
Average mass258.251
Product ions126
Normalized LC elution time *0,55 (Kellner 2014); 0,54 (Kellner 2014)
LC elution order/characteristicsbetween C and U (Kellner 2014, 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
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 -


m3C has a positive charge at neutral pH.

Chemical groups contained

methyl groupmethyl at aromatic N

Reactions producing 3-methylcytidine


Reactions starting from 3-methylcytidine


Last modification of this entry: Sept. 22, 2023