Modomics - A Database of RNA Modifications


Full name2'-O-methyluridine 5-oxyacetic acid methyl ester
IUPAC namemethyl 2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]oxyacetate
Short namemcmo5Um
MODOMICS code0503U
Nature of the modified residueNatural
RNAMods codeϿ
Residue unique ID179
Found in RNAYes
Related nucleotides369

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)3
PDB no exac match , link to the most similar ligand CM0
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
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(COc1cn(C2OC(CO)C(O)C2OC)c(=O)[nH]c1=O)=O tautomer #0
COC(=COc1cn(C2OC(CO)C(O)C2OC)c(=O)[nH]c1=O)O tautomer #1
COC(COc1cn(C2OC(CO)C(O)C2OC)c(O)nc1=O)=O tautomer #2
COC(COc1cn(C2OC(CO)C(O)C2OC)c(=O)nc1O)=O tautomer #3
COC(=COc1cn(C2OC(CO)C(O)C2OC)c(O)nc1=O)O tautomer #4
COC(=COc1cn(C2OC(CO)C(O)C2OC)c(=O)nc1O)O tautomer #5
Tautomer image Show Image

Predicted CYP Metabolic Sites

mcmo5Um mcmo5Um mcmo5Um

* 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
[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.

Reactions producing 2'-O-methyluridine 5-oxyacetic acid methyl ester



Title Authors Journal Details PubMed Id DOI
Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons Sakai Y, Miyauchi K, Kimura S, Suzuki T. Nucleic Acids Res. [details] 26681692 10.1093/nar/gkv1470

Last modification of this entry: Sept. 29, 2021

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