Summary

Full nameN4,N4,2'-O-trimethylcytidine
IUPAC name4-(dimethylamino)-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidin-2-one
Short namem4,4Cm
MODOMICS code044C
Synonyms
1-((2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-4-(dimethylamino)pyrimidin-2(1H)-one
34218-81-0
4-(dimethylamino)-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]pyrimidin-2-one
4-(dimethylamino)-1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)pyrimidin-2(1H)-one
AC1MIYQS
C12-H19-N3-O5
CID3082389
Cytidine, N,N-dimethyl-2'-O-methyl-
Cytidine,N,N-dimethyl-2'-O-methyl-
DTXSID60187801
N(4), N(4), O(2')-trimethylcytidine
N(4),N(4),O(2')-Trimethylcytidine
N,N,2'-O-Trimethylcytidine
N,N-diMethyl-2'-O-Methylcytidine
Nno-tmc
SCHEMBL14916587
ZINC33903022

Nature of the modified residueNatural
RNAMods codeβ
Residue unique ID69
Found in RNAYes
Related nucleotides427
Enzymes RsmH (Escherichia coli)
Found in phylogenyEubacteria

Chemical information

Sum formulaC12H19N3O5
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2c(=O)nc(N(C)C)cc2)O[C@H](CO)[C@H]1O
logP-1.4251
TPSA97.05
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)2
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/C12H19N3O5/c1-14(2)8-4-5-15(12(18)13-8)11-10(19-3)9(17)7(6-16)20-11/h4-5,7,9-11,16-17H,6H2,1-3H3/t7-,9-,10-,11-/m1/s1
InChIKeyWFCJCYSSTXNUED-QCNRFFRDSA-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(n2c(=O)nc(N(C)C)cc2)OC(CO)C1O tautomer #0

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m4,4Cm m4,4Cm m4,4Cm

* 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 mass285.1325
Average mass285.296
[M+H]+286.1403
Product ions140
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 O2
methyl groupmethyl at other N
methyl groupsecond methyl at other N

Reactions producing N4,N4,2'-O-trimethylcytidine

Name
m4Cm:m4,4Cm
m4,4C:m4,4Cm

Last modification of this entry: Sept. 29, 2021


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