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 namemethylated undermodified hydroxywybutosine
Short nameOHyWy
MODOMICS code new2000003480G
MODOMICS code3480G
Nature of the modified residueNatural
RNAMods codey
Residue unique ID160
Found in RNAYes
Related nucleotides421

Chemical information

Sum formulaC19H26N6O8
Type of moietynucleoside
Degeneracynot applicable
Number of atoms33
Number of Hydrogen Bond Acceptors 1 (HBA1)11
Number of Hydrogen Bond Acceptors 2 (HBA2)14
Number of Hydrogen Bond Donors (HBD)5
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 

* 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
Cn1c2nc(C)c(CC(=O)C(N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #0
Cn1c2nc(C)c(CC(O)C(=N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #1
Cn1c2nc(C)c(CC(O)C(N)C(OC)=O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #2
Cn1c2nc(C)c(C=C(O)C(N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #3
Cn1c2nc(C)c(CC(O)C(N)=C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #4
Cn1c2nc(C)c(CC(O)=C(N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #5
CN1C2=NC(C)C(=CC(=O)C(N)C(OC)O)N2C(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #6
Tautomer image Show Image

Predicted CYP Metabolic Sites


* 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 mass466.1812
Average mass466.445
Product ions335
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 methylated undermodified hydroxywybutosine


Reactions starting from methylated undermodified hydroxywybutosine


Last modification of this entry: Sept. 22, 2023