Summary

Full name5-methylaminomethyl-2-thiouridine
Short namemnm5s2U
MODOMICS code2511U
Nature of the modified residueNatural
RNAMods codeS
Residue unique ID110
Found in RNAYes
Related nucleotides402
Enzymes MnmCD (Escherichia coli)
MnmD (Aquifex aeolicus)
MnmA (Escherichia coli)
Mtu1 (Saccharomyces cerevisiae)
TrmU (Homo sapiens)
Found in phylogenyEubacteria, Eukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H17N3O5S
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3036488
SMILESCNCc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O
logP-1.3723
TPSA151.83
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand U8U
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0011610
InChIInChI=1S/C11H17N3O5S/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
InChIKeyHXVKEKIORVUWDR-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(=S)[nH]c1=O tautomer #0
CNCc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O tautomer #1
CNCc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mnm5s2U mnm5s2U mnm5s2U

* 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 mass303.0889
Average mass303.335
[M+H]+304.0967
Product ions172/255/273/141
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 atomsulfur
methyl groupmethyl at aromatic C
othersecondary amine

Reactions producing 5-methylaminomethyl-2-thiouridine

Name
nm5s2U:mnm5s2U
mnm5U:mnm5s2U

Reactions starting from 5-methylaminomethyl-2-thiouridine

Name
mnm5s2U:mnm5se2U
mnm5s2U:mnm5ges2U

Last modification of this entry: Sept. 29, 2021


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