Summary

Full nameN4,2'-O-dimethylcytidine
IUPAC name1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-4-(methylamino)pyrimidin-2-one
Short namem4Cm
MODOMICS code04C
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 residueNatural
RNAMods codeλ
Residue unique ID39
Found in RNAYes
Related nucleotides208
Enzymes RsmI (Escherichia coli)
RsmH (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typesrRNA

Chemical information

Sum formulaC11H17N3O5
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2ccc(NC)nc2=O)O[C@H](CO)[C@H]1O
logP-1.3764
TPSA105.84
Number of atoms19
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 exac match, link to the most similar ligand HMDB0000089
InChIInChI=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
InChIKeyBNXGRQLXOMSOMV-PEBGCTIMSA-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
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
m4Cm m4Cm m4Cm

* 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 mass271.1168
Average mass271.27
[M+H]+272.1246
Product ions126
Normalized LC elution time *1,20 (Kellner 2014)
LC elution order/characteristicsbetween 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

TypeSubtype
methyl groupmethyl at O2
methyl groupmethyl 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. 29, 2021


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