Modomics - A Database of RNA Modifications


Full nameuridine 5-oxyacetic acid methyl ester
Short namemcmo5U
MODOMICS code new2000000503U
Nature of the modified residueNatural
RNAMods codeυ
Residue unique ID58
Found in RNAYes
Related nucleotides425
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H16N2O9
Type of moietynucleoside
Degeneracynot applicable
PubChem ID191808
Number of atoms23
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 CM0
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 

* 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)C2O)c(=O)[nH]c1=O)=O tautomer #0
COC(=COc1cn(C2OC(CO)C(O)C2O)c(=O)[nH]c1=O)O tautomer #1
COC(COc1cn(C2OC(CO)C(O)C2O)c(O)nc1=O)=O tautomer #2
COC(COc1cn(C2OC(CO)C(O)C2O)c(=O)nc1O)=O tautomer #3
COC(=COc1cn(C2OC(CO)C(O)C2O)c(O)nc1=O)O tautomer #4
COC(=COc1cn(C2OC(CO)C(O)C2O)c(=O)nc1O)O tautomer #5
Tautomer image Show Image

Predicted CYP Metabolic Sites

mcmo5U mcmo5U mcmo5U

* 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 mass332.0856
Average mass332.263
Product ions183/201/297/315/129
Normalized LC elution time *1,47 (Kellner 2014)
LC elution order/characteristicsbetween A and m6A (Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -


Unstable under usual methods of detection, not easily detectable (Glenn Bjork, personal communication). cmo5U (and mcmo5U) is a modification characteristic for gram negative bacteria (E. coli, Protebacteria). Gram positive bacteria (B. subtilis, Firmicutes) have mo5U in this position.

Chemical groups contained


Reactions producing uridine 5-oxyacetic acid methyl ester


Reactions starting from uridine 5-oxyacetic acid methyl ester



Title Authors Journal Details PubMed Id DOI
The identification of the tRNA substrates for the supK tRNA methylase. Pope WT, Brown A, Reeves RH Nucleic Acids Res [details] 347399 -

Last modification of this entry: Sept. 22, 2023