Modomics - A Database of RNA Modifications

m4C
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

Summary

Full nameN4-methylcytidine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(methylamino)pyrimidin-2-one
Short namem4C
MODOMICS code new2000000004C
MODOMICS code4C
Synonyms
10578-79-7
106542-80-7
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(methylamino)pyrimidin-2-one
1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-4-(methylamino)pyrimidin-2(1H)-one
1-((2R,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-4-(methylamino)pyrimidin-2(1H)-one
1303AA
1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(methylamino)pyrimidin-2-one
4-Methylcytidine
AC1L2QU4
AC1Q6C4G
AC-32336
AJ-55410
AKOS016011534
AR-1I3429
C10-H15-N3-O5
C10H15N3O5
CID101436
CTK0H8883
Cytidine, N-methyl-
DS-6291
DTXSID20147340
MFCD23701766
N-4-Methylcytidine
N4-Methylcytidine
N(4)-Methylcytidine
n-methylcytidine
NSC 518744
NSC518744
SCHEMBL157772
ST24048770
ZINC5996572
Nature of the modified residueNatural
RNAMods codeν
Residue unique ID9
Found in RNAYes
Related nucleotides281
Enzymes CMAL (Arabidopsis thaliana)
RsmH (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typesrRNA

Chemical information

Sum formulaC10H15N3O5
Type of moietynucleoside
Degeneracynot applicable
SMILESCNc1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1
logP-2.0305
TPSA116.84
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
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
InChIInChI=1S/C10H15N3O5/c1-11-6-2-3-13(10(17)12-6)9-8(16)7(15)5(4-14)18-9/h2-3,5,7-9,14-16H,4H2,1H3,(H,11,12,17)/t5-,7-,8-,9-/m1/s1
InChIKeyLZCNWAXLJWBRJE-ZOQUXTDFSA-N
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

Tautomers SMILES
CN=c1[nH]c(=O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #0
CNc1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #1
CN=c1nc(O)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m4C m4C m4C

* 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 mass257.243
[M+H]+258.109
Product ions126
Normalized LC elution time * not available
LC elution order/characteristics not available

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

Chemical groups contained

TypeSubtype
methyl groupmethyl at other N

Reactions producing N4-methylcytidine

Name
C:m4C

Reactions starting from N4-methylcytidine

Name
m4C:m4Cm
m4C:m4,4C

Last modification of this entry: Sept. 22, 2023