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

See the molecule on the similarity map

Summary

Full name	N4-methylcytidine
IUPAC name	1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(methylamino)pyrimidin-2-one
Short name	m4C
MODOMICS code new	2000000004C
MODOMICS code	4C
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 residue	Natural
RNAMods code	ν
Residue unique ID	9
Found in RNA	Yes
Related nucleotides	281
Enzymes	CMAL (Arabidopsis thaliana) METTL15 (Mus musculus) RsmH (Escherichia coli)
Found in phylogeny	Eubacteria
Found naturally in RNA types	rRNA

Chemical information

Sum formula	C10H15N3O5
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CNc1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1
logP	-2.0305
TPSA	116.84
Number of atoms	18
Number of Hydrogen Bond Acceptors 1 (HBA1)	7
Number of Hydrogen Bond Acceptors 2 (HBA2)	8
Number of Hydrogen Bond Donors (HBD)	4
InChI	InChI=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
InChIKey	LZCNWAXLJWBRJE-ZOQUXTDFSA-N
Search the molecule in external databases	ChEMBL ChemAgora PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	101436
PubChem SIDs	10232043 15070134 44431467 57337379 74642989 103816393 104364297 117588129 128562131 135059603 140033892 143178791 162474997 163850446 171579027 189053749 223564581 226521601 249867859 250217078 252228354 252414863 252464702 255444791 257894762 274046820 275926161 297453032 307081829 312605608 315670145 315707950 319134781 319460292 321932182 340570025 341274099 342526824 342526825 346698310 348530313 354314538 355182536 355207376 364121860 374092619 374370630 375360528 376040223 377419311 381990130 383452050 388968399 404823486 406677383 424592044 434696420 436395698 439450949 440684228 440703507 441236939 443498304

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

QM Data:

Dipole Magnitude [D]:	8.763385323
Energy [Eh]:	-930.155905535025
HOMO [eV]:	-9.0524
LUMO [eV]:	1.0273
Gap [eV]:	10.0797

Download QM Data:

Cube	.cube
Charges	charge.txt

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

^* 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 mass	257.1012
Average mass	257.243
[M+H]⁺	258.109
Product ions	126
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

Type	Subtype
methyl group	methyl 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. 15, 2025