5TG4

OXA-24/40 in Complex with Boronic Acid BA16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Exploring the potential of boronic acids as inhibitors of OXA-24/40 beta-lactamase.

Werner, J.P.Mitchell, J.M.Taracila, M.A.Bonomo, R.A.Powers, R.A.

(2017) Protein Sci 26: 515-526

  • DOI: https://doi.org/10.1002/pro.3100
  • Primary Citation of Related Structures:  
    5TG4, 5TG5, 5TG6, 5TG7

  • PubMed Abstract: 

    β-lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β-lactams is the expression of β-lactamase enzymes. To overcome β-lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β-lactamases also contain the characteristic β-lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non-β-lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β-lactamase inhibitors, nor are they effectively inhibited by the newest, non-β-lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β-lactamases, and are not extensively characterized as inhibitors of class D β-lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β-lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA-24/40. Several compounds were identified as effective inhibitors of OXA-24/40, with K i values as low as 5 μM. The X-ray crystal structures of OXA-24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β-lactamases.


  • Organizational Affiliation

    Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase245Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33bla-OXA-40blaOXA-24blaOXA-40oxa-24oxa40
EC: 3.5.2.6
UniProt
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Explore Q8RLA6 
Go to UniProtKB:  Q8RLA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RLA6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JW1
Query on JW1

Download Ideal Coordinates CCD File 
B [auth A]{3-[(tert-butoxycarbonyl)amino]phenyl}boronic acid
C11 H16 B N O4
CWLNHPXWZRALFS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
3GR
Query on 3GR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
D-Glyceraldehyde
C3 H6 O3
MNQZXJOMYWMBOU-VKHMYHEASA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
MEE
Query on MEE

Download Ideal Coordinates CCD File 
K [auth A]METHANETHIOL
C H4 S
LSDPWZHWYPCBBB-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
A
L-PEPTIDE LINKINGC4 H9 N O2ALA
KCX
Query on KCX
A
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.113 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.347α = 90
b = 102.347β = 90
c = 85.438γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States2R15AI094489

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-08
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2023-11-15
    Changes: Data collection