4HEF

Strcuture of avibactam bound to Pseudomonas aeruginosa AmpC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insight into Potent Broad-Spectrum Inhibition with Reversible Recyclization Mechanism: Avibactam in Complex with CTX-M-15 and Pseudomonas aeruginosa AmpC beta-Lactamases

Lahiri, S.D.Mangani, S.Durand-Reville, T.Benvenuti, M.De Luca, F.Sanyal, G.Docquier, J.D.

(2013) Antimicrob.Agents Chemother. 57: 2496-2505

  • DOI: 10.1128/AAC.02247-12
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although β-lactams have been the most effective class of antibacterial agents used in clinical practice for the past half century, their effectiveness on Gram-negative bacteria has been eroded due to the emergence and spread of β-lactamase enzymes th ...

    Although β-lactams have been the most effective class of antibacterial agents used in clinical practice for the past half century, their effectiveness on Gram-negative bacteria has been eroded due to the emergence and spread of β-lactamase enzymes that are not affected by currently marketed β-lactam/β-lactamase inhibitor combinations. Avibactam is a novel, covalent, non-β-lactam β-lactamase inhibitor presently in clinical development in combination with either ceftaroline or ceftazidime. In vitro studies show that avibactam may restore the broad-spectrum activity of cephalosporins against class A, class C, and some class D β-lactamases. Here we describe the structures of two clinically important β-lactamase enzymes bound to avibactam, the class A CTX-M-15 extended-spectrum β-lactamase and the class C Pseudomonas aeruginosa AmpC β-lactamase, which together provide insight into the binding modes for the respective enzyme classes. The structures reveal similar binding modes in both enzymes and thus provide a rationale for the broad-spectrum inhibitory activity of avibactam. Identification of the key residues surrounding the binding pocket allows for a better understanding of the potency of this scaffold. Finally, avibactam has recently been shown to be a reversible inhibitor, and the structures provide insights into the mechanism of avibactam recyclization. Analysis of the ultra-high-resolution CTX-M-15 structure suggests how the deacylation mechanism favors recyclization over hydrolysis.


    Organizational Affiliation

    Infection Biosciences, AstraZeneca R&D Boston, Waltham, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
360Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: ampC
EC: 3.5.2.6
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P24735
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NXL
Query on NXL

Download SDF File 
Download CCD File 
A
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
avibactam, bound form, NXL104, bound form
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.880α = 90.00
b = 71.200β = 90.00
c = 106.250γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-03 
  • Released Date: 2013-06-05 
  • Deposition Author(s): Lahiri, S.D.

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Non-polymer description
  • Version 1.2: 2018-02-07
    Type: Experimental preparation