PDB Entry (6i9a)
PDB ID: 6i9a Resolution: 1.2 Å Exp. Method: X-RAY DIFFRACTION
PMID: 30894633 DOI: 10.1038/s41598-019-41354-3
Protein
Protein Name: Lys-gingipain W83
Uniprot ID/ACC: Q51817 (KGP83_PORGN) Organism: Porphyromonas gingivalis
Gene Symbol: kgp Gene ID: -
Protein Class: HYDROLASE
Ligand
Ligand Name:   KYT-36
Canonical SMILES:   CN(NC(=O)CC[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](CCCCN)C(=O)C(=O)NCc1ccccc1)c1ccccc1
Standard InChI:   InChI=1S/C34H42N6O6/c1-40(27-17-9-4-10-18-27)39-30(41)21-20-29(38-34(45)46-24-26-15-7-3-8-16-26)32(43)37-28(19-11-12-22-35)31(42)33(44)36-23-25-13-5-2-6-14-25/h2-10,13-18,28-29H,11-12,19-24,35H2,1H3,(H,36,44)(H,37,43)(H,38,45)(H,39,41)/t28-,29-/m0/s1
HET Code:   H8E PubChem:   11273632
DrugBank:   - ChEMBL:   -
Molecular Formula:   C34H42N6O6 Mol. Weight:   630.3166 logP:   2.7285
HBD:   5 HBA:   8
#Rotatable Bonds:   18 TPSA:   171.96
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Hemi(thio)acetalization CYS 477 A 32.43 - Ketone
Binding Affinity
-