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

Summary

Full name5-methylaminomethyl-2-selenouridine
Short namemnm5se2U
MODOMICS code new2000020511U
MODOMICS code20511U
Nature of the modified residueNatural
RNAMods code
Residue unique ID78
Found in RNAYes
Related nucleotides401
Enzymes MnmCD (Escherichia coli)
MnmH (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H17N3O5Se
Type of moietynucleoside
Degeneracynot applicable
PubChem ID6336326
SMILESCNCc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=[Se])[nH]c1=O
logP-2.4013
TPSA119.74
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand 38T
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C11H17N3O5Se/c1-12-2-5-3-14(11(20)13-9(5)18)10-8(17)7(16)6(4-15)19-10/h3,6-8,10,12,15-17H,2,4H2,1H3,(H,13,18,20)/t6-,7-,8-,10-/m1/s1
InChIKeyLKYNRXHIWDCZMH-FDDDBJFASA-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
CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])[nH]c1=O tautomer #0
CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])nc1O tautomer #1
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mnm5se2U mnm5se2U mnm5se2U

* 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 mass349.0341
Average mass350.23
[M+H]+350.0419
Product ions218
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
methyl groupmethyl at aromatic C
othersecondary amine

Reactions producing 5-methylaminomethyl-2-selenouridine

Name
nm5se2U:mnm5se2U
mnm5s2U:mnm5se2U

Last modification of this entry: Sept. 22, 2023