PDB Entry (3pa8)
PDB ID: 3pa8 Resolution: 2.0 Å Exp. Method: X-RAY DIFFRACTION
PMID: 21095570 DOI: 10.1016/j.chembiol.2010.09.011
Protein
Protein Name: Toxin B
Uniprot ID/ACC: Q189K3 (Q189K3_CLOD6) Organism: Clostridioides difficile (strain 630) (Peptoclostridium difficile)
Gene Symbol: tcdB Gene ID: -
Protein Class: HYDROLASE
Ligand
Ligand Name:   Ac-GSL-AOMK
Canonical SMILES:   CC(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)C(=O)COC(=O)c1c(C)cccc1C
Standard InChI:   InChI=1S/C23H33N3O7/c1-13(2)9-17(26-22(31)18(11-27)25-20(30)10-24-16(5)28)19(29)12-33-23(32)21-14(3)7-6-8-15(21)4/h6-8,13,17-18,27H,9-12H2,1-5H3,(H,24,28)(H,25,30)(H,26,31)/t17-,18-/m0/s1
HET Code:   621 PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C23H33N3O7 Mol. Weight:   463.23184 logP:   0.17344
HBD:   4 HBA:   7
#Rotatable Bonds:   12 TPSA:   150.9
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Nucleophilic Aliphatic Subsititution CYS 155 A 29.97 11.28 Acyloxymethyl Carbonyl
Binding Affinity
Database Name Value
PDBBind IC50 : 1780 nM