PDB Entry (3pa8) |
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PDB ID: 3pa8 | Resolution: 2.0 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 21095570 | DOI: 10.1016/j.chembiol.2010.09.011 | |
Protein |
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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 |
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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 |
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Database Name | Value |
PDBBind | IC50 : 1780 nM |