Modomics - A Database of RNA Modifications


Full name7-aminocarboxypropylwyosine methyl ester
Short nameyW-58
Nature of the modified residueNatural
RNAMods code
Residue unique ID112
Found in RNAYes
Related nucleotides407
Enzymes TYW4 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota

Chemical information

Sum formulaC19H26N6O7
Type of moietynucleoside
Degeneracynot applicable
Number of atoms32
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)13
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand YG
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0039126
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(CCC(=N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #0
Cn1c2nc(C)c(CCC(N)C(OC)=O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #1
Cn1c2nc(C)c(CC=C(N)C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #2
Cn1c2nc(C)c(CCC(N)=C(OC)O)n2c(=O)c3ncn(C4OC(CO)C(O)C4O)c13 tautomer #3

Tautomer image Show Image

Predicted CYP Metabolic Sites

yW-58 yW-58 yW-58

* 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 mass450.1863
Average mass450.446
Product ions319
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.

Chemical groups contained

aminoacyl groupglutamyl
methyl groupmethyl at aromatic N
ring modificationwyosine

Reactions producing 7-aminocarboxypropylwyosine methyl ester


Reactions starting from 7-aminocarboxypropylwyosine methyl ester


Last modification of this entry: Sept. 29, 2021

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