Summary

Full name5-formyl-2'-O-methylcytidine
IUPAC name4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2-oxopyrimidine-5-carbaldehyde
Short namef5Cm
MODOMICS code071C
Synonyms
176858-79-0
4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2-oxopyrimidine-5-carbaldehyde
5-formyl-2'-o-methylcytidine
cytidine, 5-formyl-2'-O-methyl-
SCHEMBL1274188

Nature of the modified residueNatural
RNAMods code°
Residue unique ID104
Found in RNAYes
Related nucleotides397
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H15N3O6
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2cc(C=O)c(N)nc2=O)O[C@H](CO)[C@H]1O
logP-1.5152
TPSA136.9
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)3
PDB no exac match , link to the most similar ligand LKC
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000982
InChIInChI=1S/C11H15N3O6/c1-19-8-7(17)6(4-16)20-10(8)14-2-5(3-15)9(12)13-11(14)18/h2-3,6-8,10,16-17H,4H2,1H3,(H2,12,13,18)/t6-,7-,8-,10-/m1/s1
InChIKeyYBBDRHCNZBVLGT-FDDDBJFASA-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(n2cc(C=O)c(=N)[nH]c2=O)OC(CO)C1O tautomer #0
COC1C(n2cc(C=O)c(N)nc2=O)OC(CO)C1O tautomer #1
COC1C(n2cc(C=O)c(=N)nc2O)OC(CO)C1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
f5Cm f5Cm f5Cm

* 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 mass285.0961
Average mass285.253
[M+H]+286.1039
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
otherformyl

Reactions producing 5-formyl-2'-O-methylcytidine

Name
f5C:f5Cm
Cm:f5Cm

Last modification of this entry: Sept. 29, 2021


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