8SZM image
Deposition Date 2023-05-30
Release Date 2024-09-18
Last Version Date 2024-09-25
Entry Detail
PDB ID:
8SZM
Keywords:
Title:
Crystal structure of E. coli ClpP protease in complex with phosphine oxide compound ACP6-12
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.35 Å
R-Value Free:
0.26
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:ATP-dependent Clp protease proteolytic subunit
Gene (Uniprot):clpP_2
Chain IDs:A (auth: H), B (auth: I), C (auth: J), D (auth: K), E (auth: L), F (auth: M), G (auth: N), H (auth: A), I (auth: B), J (auth: C), K (auth: D), L (auth: E), M (auth: F), N (auth: G), O, P, Q, R, S, T, U, V, W, X, Y, Z, AA (auth: a), BA (auth: b)
Chain Length:207
Number of Molecules:28
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases.
J.Med.Chem. 67 15131 15147 (2024)
PMID: 39221504 DOI: 10.1021/acs.jmedchem.4c00773

Abstact

A series of arylsulfones and heteroarylsulfones have previously been demonstrated to dysregulate the conserved bacterial ClpP protease, causing the unspecific degradation of essential cellular housekeeping proteins and ultimately resulting in cell death. A cocrystal structure of a 2-β-sulfonylamide analog, ACP1-06, with Escherichia coli ClpP showed that its 2-pyridyl sulfonyl substituent adopts two orientations in the binding site related through a sulfone bond rotation. From this, a new bis-aryl phosphine oxide scaffold, designated as ACP6, was designed based on a "conformation merging" approach of the dual orientation of the ACP1-06 sulfone. One analog, ACP6-12, exhibited over a 10-fold increase in activity over the parent ACP1-06 compound, and a cocrystal X-ray structure with ClpP confirmed its predicted binding conformation. This allowed for a comparative analysis of how different ligand classes bind to the hydrophobic binding site. The study highlights the successful application of structure-based rational design of novel phosphine oxide-based antibiotics.

Legend

Protein

Chemical

Disease

Primary Citation of related structures