Modomics - A Database of RNA Modifications

hm5Cm
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 name2'-O-methyl-5-hydroxymethylcytidine
IUPAC name4-amino-1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
Short namehm5Cm
MODOMICS code new2000009051C
MODOMICS code051C
Synonyms
2'-O-Methyl-5-hydroxymethylcytidine
J3.656.840B
Nature of the modified residueNatural
RNAMods code¡
Residue unique ID183
Found in RNAYes
Related nucleotides366

Chemical information

Sum formulaC11H17N3O6
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2cc(CO)c(N)nc2=O)O[C@H](CO)[C@H]1O
logP-1.8354
TPSA140.06
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)4
PDB no exac match , link to the most similar ligand LKC
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C11H17N3O6/c1-19-8-7(17)6(4-16)20-10(8)14-2-5(3-15)9(12)13-11(14)18/h2,6-8,10,15-17H,3-4H2,1H3,(H2,12,13,18)/t6-,7-,8-,10-/m1/s1
InChIKeyYHOUCWSAAAAILW-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(CO)c(=N)[nH]c2=O)OC(CO)C1O tautomer #0
COC1C(n2cc(CO)c(N)nc2=O)OC(CO)C1O tautomer #1
COC1C(n2cc(CO)c(=N)nc2O)OC(CO)C1O tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
hm5Cm hm5Cm hm5Cm

* 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 mass287.1117
Average mass287.269
[M+H]+ not available
Product ions not available
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.

Publications

Title Authors Journal Details PubMed Id DOI
2'-O-Methyl-5-hydroxymethylcytidine: A Second Oxidative Derivative of 5-Methylcytidine in RNA. Huber SM, van Delft P, Tanpure A, Miska EA, Balasubramanian S... J Am Chem Soc [details] 28107630 -

Last modification of this entry: Sept. 22, 2023