7AUX

Crystal structure of OXA-48 beta-lactamase in the complex with the inhbitor ID2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of Novel Chemical Series of OXA-48 beta-Lactamase Inhibitors by High-Throughput Screening.

Garofalo, B.Prati, F.Buonfiglio, R.Coletta, I.D'Atanasio, N.Molteni, A.Carettoni, D.Wanke, V.Pochetti, G.Montanari, R.Capelli, D.Milanese, C.Di Giorgio, F.P.Ombrato, R.

(2021) Pharmaceuticals (Basel) 14

  • DOI: https://doi.org/10.3390/ph14070612
  • Primary Citation of Related Structures:  
    7AUX, 7AW5

  • PubMed Abstract: 

    The major cause of bacterial resistance to β-lactams is the production of hydrolytic β-lactamase enzymes. Nowadays, the combination of β-lactam antibiotics with β-lactamase inhibitors (BLIs) is the main strategy for overcoming such issues. Nevertheless, particularly challenging β-lactamases, such as OXA-48, pose the need for novel and effective treatments. Herein, we describe the screening of a proprietary compound collection against Klebsiella pneumoniae OXA-48, leading to the identification of several chemotypes, like the 4-ideneamino-4H-1,2,4-triazole (SC_2) and pyrazolo[3,4-b]pyridine (SC_7) cores as potential inhibitors. Importantly, the most potent representative of the latter series (ID2, AC 50 = 0.99 μM) inhibited OXA-48 via a reversible and competitive mechanism of action, as demonstrated by biochemical and X-ray studies; furthermore, it slightly improved imipenem's activity in Escherichia coli ATCC BAA-2523 β-lactam resistant strain. Also, ID2 showed good solubility and no sign of toxicity up to the highest tested concentration, resulting in a promising starting point for further optimization programs toward novel and effective non-β-lactam BLIs.


  • Organizational Affiliation

    Angelini Pharma S.p.A., Global R&D External Innovation, Viale Amelia 70, 00181 Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
242Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48blaOXA-48KPE71T_00045
EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LKW
Query on LKW

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
6-(4-carboxyphenyl)-3-(4-ethylphenyl)-2~{H}-pyrazolo[3,4-b]pyridine-4-carboxylic acid
C22 H17 N3 O4
AJRMTRZJIPBKHX-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.41α = 90
b = 72.63β = 90
c = 125.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description