5TG7

OXA-24/40 in Complex with Boronic Acid BA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/pro.3100
  • Primary Citation of Related Structures:  

  • 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 resistan ...

    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 Ki 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
245Acinetobacter baumanniiMutation(s): 0 
Gene Names: blaOXA-33 (bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40)
Find proteins for Q8RLA6 (Acinetobacter baumannii)
Go to UniProtKB:  Q8RLA6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
JW3
Query on JW3

Download SDF File 
Download CCD File 
A
(3-{[(furan-2-yl)methyl]carbamoyl}phenyl)boronic acid
C12 H12 B N O4
BYRIHRGFMYXTLC-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download SDF File 
Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MEE
Query on MEE

Download SDF File 
Download CCD File 
A
METHANETHIOL
C H4 S
LSDPWZHWYPCBBB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D 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: 2.28 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.083α = 90.00
b = 103.083β = 90.00
c = 86.437γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States2R15AI094489

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-08
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence