Modomics - A Database of RNA Modifications


Full name5-(carboxyhydroxymethyl)-2'-O-methyluridine methyl ester
IUPAC namemethyl 2-hydroxy-2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetate
Short namemchm5Um
MODOMICS code new2000090522U
MODOMICS code0522U

Nature of the modified residueNatural
RNAMods codeb
Residue unique ID164
Found in RNAYes
Related nucleotides384

Chemical information

Sum formulaC13H18N2O9
Type of moietynucleoside
Degeneracynot applicable
Number of atoms24
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 38T
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
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 SMILES
COC(C(=O)C1CN(C2OC(CO)C(O)C2OC)C(=O)NC1=O)=O tautomer #0
COC(C(=O)c1cn(C2OC(CO)C(O)C2OC)c(=O)[nH]c1=O)O tautomer #1
COC(C(O)c1cn(C2OC(CO)C(O)C2OC)c(=O)[nH]c1=O)=O tautomer #2
COC(C(O)=C1CN(C2OC(CO)C(O)C2OC)C(=O)NC1=O)=O tautomer #3
COC(C(=O)C=1CN(C2OC(CO)C(O)C2OC)C(=O)NC1O)=O tautomer #4
COC(=C(O)c1cn(C2OC(CO)C(O)C2OC)c(=O)[nH]c1=O)O tautomer #5
COC(C(=O)c1cn(C2OC(CO)C(O)C2OC)c(O)nc1=O)O tautomer #6
COC(C(=O)C1CN(C2OC(CO)C(O)C2OC)C(O)=NC1=O)=O tautomer #7
COC(C(O)c1cn(C2OC(CO)C(O)C2OC)c(O)nc1=O)=O tautomer #8
COC(C(=O)c1cn(C2OC(CO)C(O)C2OC)c(=O)nc1O)O tautomer #9
COC(C(=O)C1CN(C2OC(CO)C(O)C2OC)C(=O)N=C1O)=O tautomer #10
COC(C(O)c1cn(C2OC(CO)C(O)C2OC)c(=O)nc1O)=O tautomer #11
COC(C(O)=C1CN(C2OC(CO)C(O)C2OC)C(O)=NC1=O)=O tautomer #12
COC(C(=O)C=1CN(C2OC(CO)C(O)C2OC)C(O)=NC1O)=O tautomer #13
COC(C(O)=C1CN(C2OC(CO)C(O)C2OC)C(=O)N=C1O)=O tautomer #14
COC(=C(O)c1cn(C2OC(CO)C(O)C2OC)c(O)nc1=O)O tautomer #15
COC(=C(O)c1cn(C2OC(CO)C(O)C2OC)c(=O)nc1O)O tautomer #16

Tautomer image Show Image

Predicted CYP Metabolic Sites

mchm5Um mchm5Um mchm5Um

* 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 mass346.1012
Average mass346.29
Product ions201
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.

Reactions producing 5-(carboxyhydroxymethyl)-2'-O-methyluridine methyl ester


Last modification of this entry: Sept. 22, 2023