Summary

Full name5-taurinomethyl-2-thiouridine
Short nametm5s2U
MODOMICS code254U
Nature of the modified residueNatural
RNAMods code
Residue unique ID91
Found in RNAYes
Related nucleotides403
Enzymes TrmU (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H19N3O8S2
Type of moietynucleoside
Degeneracynot applicable
SMILESOC[C@H]1O[C@@H]([n]2cc(CNCCS(O)(=O)=O)c(=O)[nH]c2=S)[C@H](O)[C@@H]1O
logP-1.0335
TPSA214.58
Number of atoms25
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)6
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/C12H19N3O8S2/c16-5-7-8(17)9(18)11(23-7)15-4-6(10(19)14-12(15)24)3-13-1-2-25(20,21)22/h4,7-9,11,13,16-18H,1-3,5H2,(H,14,19,24)(H,20,21,22)/t7-,8-,9-,11-/m1/s1
InChIKeyXMIFBEZRFMTGRL-TURQNECASA-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
OCC1OC(n2cc(CN=CCS(O)(O)=O)c(=O)[nH]c2=S)C(O)C1O tautomer #0
OCC1OC(n2cc(CNCCS(=O)(O)=O)c(=O)[nH]c2=S)C(O)C1O tautomer #1
OCC1OC(n2cc(CNC=CS(O)(O)=O)c(=O)[nH]c2=S)C(O)C1O tautomer #2
OCC1OC(n2cc(CN=CCS(O)(O)=O)c(=O)nc2S)C(O)C1O tautomer #3
OCC1OC(n2cc(CNCCS(=O)(O)=O)c(=O)nc2S)C(O)C1O tautomer #4
OCC1OC(n2cc(CNC=CS(O)(O)=O)c(=O)nc2S)C(O)C1O tautomer #5
OCC1OC(n2cc(CNCC=[SH](O)(O)=O)c(=O)[nH]c2=S)C(O)C1O tautomer #6
OCC1OC(n2cc(CNCC=[SH](O)(O)=O)c(=O)nc2S)C(O)C1O tautomer #7
OCC1OC(n2cc(CN=CCS(O)(O)=O)c(O)nc2=S)C(O)C1O tautomer #8
OCC1OC(n2cc(CNCCS(=O)(O)=O)c(O)nc2=S)C(O)C1O tautomer #9
OCC1OC(n2cc(CNC=CS(O)(O)=O)c(O)nc2=S)C(O)C1O tautomer #10
OCC1OC(n2cc(CNCC=[SH](O)(O)=O)c(O)nc2=S)C(O)C1O tautomer #11

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
tm5s2U tm5s2U tm5s2U

* 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 mass397.0614
Average mass397.425
[M+H]+398.0692
Product ions266
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
othertauryl

Reactions producing 5-taurinomethyl-2-thiouridine

Name
tm5U:tm5s2U
s2U:tm5s2U

Last modification of this entry: Sept. 29, 2021


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