Structure of PDB 8szn Chain W Binding Site BS01

Receptor Information

>8szn Chain W (length=190) Species: 487 (Neisseria meningitidis)

TVIEQSGRGERAFDIYSRLLKERIVFLVGPVTDESANLVVAQLLFLESEN
PDKDIFFYINSPGGSVTAGMSIYDTMNFIKPDVSTLCLGQAASMGAFLLS
AGEKGKRFALPNSRIMIHQPLISGGGQASDIEIHARELLKIKEKLNRLMA
KHCDRDLADLERDTDRDNFMSAEEAKEYGLIDQILENRAS

Ligand information

• Ligand ID: X3O
• InChI: InChI=1S/C25H21F9N3O2PS/c1-22(2,21(38)35-11-12-41-18-6-4-3-5-17(18)25(32,33)34)40(39,19-9-7-15(13-36-19)23(26,27)28)20-10-8-16(14-37-20)24(29,30)31/h3-10,13-14H,11-12H2,1-2H3,(H,35,38)
• InChIKey: YZQNSGLJZOYKHY-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C(=O)NCCSc1ccccc1C(F)(F)F)[P](=O)(c2ccc(cn2)C(F)(F)F)c3ccc(cn3)C(F)(F)F
  ACDLabs 12.01: O=P(c1ccc(cn1)C(F)(F)F)(c1ccc(cn1)C(F)(F)F)C(C)(C)C(=O)NCCSc1ccccc1C(F)(F)F
  OpenEye OEToolkits 2.0.7: CC(C)(C(=O)NCCSc1ccccc1C(F)(F)F)P(=O)(c2ccc(cn2)C(F)(F)F)c3ccc(cn3)C(F)(F)F
  CACTVS 3.385: CC(C)(C(=O)NCCSc1ccccc1C(F)(F)F)[P@@](=O)(c2ccc(cn2)C(F)(F)F)c3ccc(cn3)C(F)(F)F
• Formula: C25 H21 F9 N3 O2 P S
• Name: 2-{bis[5-(trifluoromethyl)pyridin-2-yl]phosphoryl}-2-methyl-N-(2-{[2-(trifluoromethyl)phenyl]sulfanyl}ethyl)propanamide
• PDB chain: 8szn Chain W Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8szn Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases.
• Resolution: 2.33 Å
• Binding residue (original residue number in PDB): R27 L28 E31 I33 F65 Y67 L95 F117 R199
• Binding residue (residue number reindexed from 1): R18 L19 E22 I24 F56 Y58 L86 F108 R188
• Annotation score: 1

External links

• PDB: RCSB:8szn, PDBe:8szn, PDBj:8szn
• PDBsum: 8szn
• PubMed: 39221504
• UniProt: Q9JZ38|CLPP_NEIMB ATP-dependent Clp protease proteolytic subunit (Gene Name=clpP)