6RTN image
Deposition Date 2019-05-24
Release Date 2019-09-11
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6RTN
Title:
Crystal structure of OXA-10 with VNRX-5133
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.17 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Beta-lactamase OXA-10
Gene (Uniprot):OXA-10
Chain IDs:A, B
Chain Length:247
Number of Molecules:2
Biological Source:Pseudomonas aeruginosa
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX A LYS modified residue
Primary Citation
Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-beta-Lactamases.
J.Med.Chem. 62 8544 8556 (2019)
PMID: 31454231 DOI: 10.1021/acs.jmedchem.9b00911

Abstact

The bicyclic boronate VNRX-5133 (taniborbactam) is a new type of β-lactamase inhibitor in clinical development. We report that VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2. VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not observed. Crystallography reveals how VNRX-5133 binds to the class D SBL OXA-10 and MBL NDM-1. The crystallographic results highlight the ability of bicyclic boronates to inhibit SBLs and MBLs via binding of a tetrahedral (sp3) boron species. The structures imply conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1, by crystallography, we observed an unanticipated VNRX-5133 binding mode involving cyclization of its acylamino oxygen onto the boron of the bicyclic core. Different side-chain binding modes for bicyclic boronates for SBLs and MBLs imply scope for side-chain optimization. The results further support the "high-energy-intermediate" analogue approach for broad-spectrum β-lactamase inhibitor development and highlight the ability of boron inhibitors to interchange between different hybridization states/binding modes.

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Primary Citation of related structures