Summary

Full name2-geranylthiouridine
Short nameges2U
MODOMICS code21U
Nature of the modified residueNatural
RNAMods codeΓ
Residue unique ID166
Found in RNAYes
Related nucleotides373
Enzymes MnmH (Escherichia coli)
Found in phylogenyEubacteria

Chemical information

Sum formulaC19H28N2O5S
Type of moietynucleoside
Degeneracynot applicable
SMILESCC(C)=CCC/C(/C)=C/CSc1nc(=O)cc[n]1[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O
logP1.6396
TPSA130.11
Number of atoms27
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)3
PDB no exac match , link to the most similar ligand URI
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0004813
InChIInChI=1S/C19H28N2O5S/c1-12(2)5-4-6-13(3)8-10-27-19-20-15(23)7-9-21(19)18-17(25)16(24)14(11-22)26-18/h5,7-9,14,16-18,22,24-25H,4,6,10-11H2,1-3H3/b13-8+/t14-,16-,17-,18-/m1/s1
InChIKeyKFZLIRUEFHTLEW-ZGFVZBPKSA-N
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

Tautomers SMILES
CC(C)=CCCC(C)=CCSc1nc(=O)ccn1C2OC(CO)C(O)C2O tautomer #0

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ges2U ges2U ges2U

* 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 mass396.1719
Average mass396.501
[M+H]+397.1797
Product ions265
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.

Comments

An intermediate in the synthesis of cmnm5ges2U and mnm5ges2U.

Chemical groups contained

TypeSubtype
sulphurthio
hydrocarbongeranyl

Reactions producing 2-geranylthiouridine

Name
s2U:ges2U

Reactions starting from 2-geranylthiouridine

Name
ges2U:cmnm5ges2U
ges2U:nm5ges2U

Publications

Title Authors Journal Details PubMed Id DOI
Discovery and biological characterization of geranylated RNA in bacteria. Dumelin CE, Chen Y, Leconte AM, Chen YG, Liu DR... Nat Chem Biol [details] 22983156 -
A gain of function mutation in a protein mediates production of novel modified nucleosides. Chen P, Crain PF, Nasvall SJ, Pomerantz SC, Bjork GR... EMBO J [details] 15861125 -

Last modification of this entry: Sept. 29, 2021


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