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

Summary

Full name	N4,2'-O-dimethylcytidine
IUPAC name	1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-(methylamino)pyrimidin-2-one
Short name	m4Cm
MODOMICS code new	2000000904C
MODOMICS code	04C
Synonyms	1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-(methylamino)pyrimidin-2-one 1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-4-(methylamino)pyrimidin-2(1H)-one 13048-95-8 AC1MIVIC C11-H17-N3-O5 CID3080688 CTK4B6750 Cytidine, N-methyl-2'-O-methyl- Cytidine,N-methyl-2'-O-methyl- DTXSID00156571 N,2'-O-Dimethylcytidine N(4), O(2')-Dimethylcytidine N(4), O(2/')-Dimethylcytidine n4-methyl-2' -O-methyl cytidine N4-Methyl-2'-O-methylcytidine N4-Methyl-2'-O-Methyl-cytidine SCHEMBL14917408
Nature of the modified residue	Natural
RNAMods code	Λ
Residue unique ID	39
Found in RNA	Yes
Related nucleotides	208
Enzymes	RsmI (Escherichia coli) RsmH (Escherichia coli)
Found in phylogeny	Eubacteria
Found naturally in RNA types	rRNA

Chemical information

Sum formula	C11H17N3O5
Type of moiety	nucleoside
Degeneracy	not applicable
SMILES	CO[C@H]1[C@H]([n]2ccc(NC)nc2=O)O[C@H](CO)[C@H]1O
logP	-1.3764
TPSA	105.84
Number of atoms	19
Number of Hydrogen Bond Acceptors 1 (HBA1)	7
Number of Hydrogen Bond Acceptors 2 (HBA2)	8
Number of Hydrogen Bond Donors (HBD)	3
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
InChI	InChI=1S/C11H17N3O5/c1-12-7-3-4-14(11(17)13-7)10-9(18-2)8(16)6(5-15)19-10/h3-4,6,8-10,15-16H,5H2,1-2H3,(H,12,13,17)/t6-,8-,9-,10-/m1/s1
InChIKey	BNXGRQLXOMSOMV-PEBGCTIMSA-N
Search the molecule in external databases	ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	3080688
PubChem SIDs	36411622 51401113 57354372 111681001 127542884 135227892 162785068 239883929 252228353 275348824 315717092 319287605 341356233 349630781 355182525 381990069 385541563 391911130 405013989 425964802 433864611 439473686 440695917 443511619

^* 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	COC1C(n2ccc(=NC)[nH]c2=O)OC(CO)C1O tautomer #0 COC1C(n2ccc(NC)nc2=O)OC(CO)C1O tautomer #1 COC1C(n2ccc(=NC)nc2O)OC(CO)C1O 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	271.1168
Average mass	271.27
[M+H]⁺	272.1246
Product ions	126
Normalized LC elution time^*	1,20 (Kellner 2014)
LC elution order/characteristics	between G and A (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	-

Chemical groups contained

Type	Subtype
methyl group	methyl at O2
methyl group	methyl at other N

Reactions producing N4,2'-O-dimethylcytidine

Name
m4C:m4Cm
Cm:m4Cm

Reactions starting from N4,2'-O-dimethylcytidine

Name
m4Cm:m4,4Cm

Last modification of this entry: Sept. 22, 2023