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 namewybutosine
IUPAC namemethyl 4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4,6-dimethyl-9-oxoimidazo[1,2-a]purin-7-yl]-2-(methoxycarbonylamino)butanoate
Short nameyW
MODOMICS code new2000003483G
MODOMICS code3483G
2-(Methoxycarbonylamino)-4-[3-(beta-D-ribofuranosyl)-4,6-dimethyl-9-oxo-4,9-dihydro-3H-imidazo[1,2-a]purine-7-yl]butyric acid methyl ester
Nature of the modified residueNatural
RNAMods codeY
Residue unique ID30
Found in RNAYes
Related nucleotides244
Enzymes TYW4 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC21H28N6O9
Type of moietynucleoside
Degeneracynot applicable
Number of atoms36
Number of Hydrogen Bond Acceptors 1 (HBA1)12
Number of Hydrogen Bond Acceptors 2 (HBA2)15
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand YG
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(N=C(C(OC)O)CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)=O tautomer #0
COC(NC(C(OC)=O)CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)=O tautomer #1
COC(NC(C(OC)O)=CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)=O tautomer #2
COC(NC(=C(OC)O)CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)=O tautomer #3
COC(=NC(C(OC)=O)CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)O tautomer #4
COC(=NC(=C(OC)O)CCc1n2c(n(c3c(c2=O)ncn3C4C(O)C(O)C(CO)O4)C)nc1C)O tautomer #5
Tautomer image Show Image

Predicted CYP Metabolic Sites

yW yW yW

* 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 mass508.1918
Average mass508.482
Product ions377
Normalized LC elution time *2,93 (Kellner 2014)
LC elution order/characteristicsafter 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 -

Chemical groups contained

aminoacyl groupglutamyl
ring modificationwyosine

Reactions producing wybutosine



Title Authors Journal Details PubMed Id DOI
Studies on polynucleotides, lxviii the primary structure of yeast phenylalanine transfer RNA. Rajbhandary UL, Chang SH, Stuart A, Faulkner RD, Hoskinson RM, Khorana HG Proc Natl Acad Sci U S A [details] 16591527 -
A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid. Thiebe R, Zachau HG Eur J Biochem [details] 5698615 -
A fluorescence assay for phenylalanine transfer RNA. Yoshikami D, Katz G, Keller EB, Dudock BS Biochim Biophys Acta [details] 5722700 -

Last modification of this entry: Sept. 22, 2023