4OOY

Avibactam and class C beta-lactamases: mechanism of inhibition, conservation of binding pocket and implications for resistance


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Avibactam and Class C beta-Lactamases: Mechanism of Inhibition, Conservation of the Binding Pocket, and Implications for Resistance.

Lahiri, S.D.Johnstone, M.R.Ross, P.L.McLaughlin, R.E.Olivier, N.B.Alm, R.A.

(2014) Antimicrob Agents Chemother 58: 5704-5713

  • DOI: https://doi.org/10.1128/AAC.03057-14
  • Primary Citation of Related Structures:  
    4OOY

  • PubMed Abstract: 

    Avibactam is a novel non-β-lactam β-lactamase inhibitor that inhibits a wide range of β-lactamases. These include class A, class C, and some class D enzymes, which erode the activity of β-lactam drugs in multidrug-resistant pathogens like Pseudomonas aeruginosa and Enterobacteriaceae spp. Avibactam is currently in clinical development in combination with the β-lactam antibiotics ceftazidime, ceftaroline fosamil, and aztreonam. Avibactam has the potential to be the first β-lactamase inhibitor that might provide activity against class C-mediated resistance, which represents a growing concern in both hospital- and community-acquired infections. Avibactam has an unusual mechanism of action: it is a covalent inhibitor that acts via ring opening, but in contrast to other currently used β-lactamase inhibitors, this reaction is reversible. Here, we present a high-resolution structure of avibactam bound to a class C β-lactamase, AmpC, from P. aeruginosa that provided insight into the mechanism of both acylation and recyclization in this enzyme class and highlighted the differences observed between class A and class C inhibition. Furthermore, variants resistant to avibactam that identified the residues important for inhibition were isolated. Finally, the structural information was used to predict effective inhibition by sequence analysis and functional studies of class C β-lactamases from a large and diverse set of contemporary clinical isolates (P. aeruginosa and several Enterobacteriaceae spp.) obtained from recent infections to understand any preexisting variability in the binding pocket that might affect inhibition by avibactam.


  • Organizational Affiliation

    Infection Innovative Medicines, AstraZeneca R&D Boston, Boston, Massachusetts, USA sushmita.lahiri@astrazeneca.com richard.alm@astrazeneca.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase359Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: ampCPA4110
EC: 3.5.2.6
UniProt
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P24735 
Go to UniProtKB:  P24735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24735
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL

Download Ideal Coordinates CCD File 
B [auth A](2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.757α = 90
b = 71.269β = 90
c = 106.129γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
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: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Non-polymer description
  • Version 1.3: 2018-02-14
    Changes: Experimental preparation
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary