Modomics - A Database of RNA Modifications

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


Full name5-methyl-2-thiouridine
Short namem5s2U
MODOMICS code new2000000025U
Nature of the modified residueNatural
RNAMods codeF
Residue unique ID3
Found in RNAYes
Related nucleotides399
Enzymes TrmU (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC10H14N2O5S
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3035361
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 2TU
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
Cc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O tautomer #0
Cc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O tautomer #1
Cc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

m5s2U m5s2U m5s2U

* 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 mass274.0623
Average mass274.294
Product ions143
Normalized LC elution time *1,36 (Kellner 2014)
LC elution order/characteristicsbetween G and A (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
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Chemical groups contained

heavy atomsulfur
methyl groupmethyl at aromatic C

Reactions producing 5-methyl-2-thiouridine


Last modification of this entry: Sept. 22, 2023