Summary

Full nameN4,N4-dimethylcytidine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(dimethylamino)pyrimidin-2-one
Short namem4,4C
MODOMICS code44C
Synonyms
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-(dimethylamino)pyrimidin-2-one
1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-4-(dimethylamino)pyrimidin-2(1H)-one
13007-43-7
4-(Dimethylamino)-1-(beta-D-ribofuranosyl)pyrimidin-2(1H)-one
CTK0C1362
Cytidine, N,N-dimethyl-
DTXSID50707012
n4,n4-dimethylcytidine
n,n-dimethylcytidine
Q15632686
SCHEMBL3863688

Nature of the modified residueNatural
RNAMods codeμ
Residue unique ID15
Found in RNAYes
Related nucleotides250
Enzymes RsmH (Escherichia coli)
Found in phylogenyEubacteria

Chemical information

Sum formulaC11H17N3O5
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3082389
SMILESCN(c1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1)C
logP-2.0792
TPSA108.05
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/c1-13(2)7-3-4-14(11(18)12-7)10-9(17)8(16)6(5-15)19-10/h3-4,6,8-10,15-17H,5H2,1-2H3/t6-,8-,9-,10-/m1/s1
InChIKeyGFCDNWCHLZESES-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
CN(c1nc(=O)n(C2C(O)C(O)C(CO)O2)cc1)C tautomer #0

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m4,4C m4,4C m4,4C

* 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 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 other N
methyl groupsecond methyl at other N

Reactions producing N4,N4-dimethylcytidine

Name
m4C:m4,4C

Reactions starting from N4,N4-dimethylcytidine

Name
m4,4C:m4,4Cm

Last modification of this entry: Sept. 29, 2021


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