Summary

Full name2-selenouridine
Short namese2U
MODOMICS code20U
Synonyms
1-beta-D-Ribofuranosyl-2,3-dihydro-2-selenoxopyrimidine-4(1H)-one
2-selenouridine
J3.548.109E
SCHEMBL7180415

Nature of the modified residueNatural
RNAMods codeω
Residue unique ID94
Found in RNAYes
Related nucleotides230
Found in phylogenyEubacteria

Chemical information

Sum formulaC9H12N2O5Se
Type of moietynucleoside
Degeneracynot applicable
SMILESO[C@H]1[C@H]([n]2ccc(=O)[nH]c2=[Se])O[C@H](CO)[C@H]1O
logP-2.5116
TPSA107.71
Number of atoms17
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)6
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand URI
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C9H12N2O5Se/c12-3-4-6(14)7(15)8(16-4)11-2-1-5(13)10-9(11)17/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,17)/t4-,6-,7-,8-/m1/s1
InChIKeyRFZIZXWYWPNBGL-XVFCMESISA-N
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

Tautomers SMILES
OC1C(n2ccc(=O)[nH]c2=[Se])OC(CO)C1O tautomer #0
OC1C(n2ccc(O)nc2=[Se])OC(CO)C1O tautomer #1

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
se2U se2U se2U

* 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 mass305.9919
Average mass307.162
[M+H]+306.9997
Product ions175
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

TypeSubtype
heavy atomselenium

Reactions producing 2-selenouridine

Name
s2U:se2U

Reactions starting from 2-selenouridine

Name
se2U:nm5se2U
se2U:cmnm5se2U

Last modification of this entry: Sept. 29, 2021


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