4WYY

Crystal Structure of P. aeruginosa AmpC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine beta-Lactamase Inhibitors.

McKinney, D.C.Zhou, F.Eyermann, C.J.Ferguson, A.D.Prince, D.B.Breen, J.Giacobbe, R.A.Lahiri, S.Verheijen, J.C.

(2015) ACS Infect Dis 1: 310-316

  • DOI: 10.1021/acsinfecdis.5b00031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derive ...

    Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derived β-lactamase inhibitors in which crystal structures and computational modeling aided in the rational design of analogues with improved spectrum of activity against class A, C, and D enzymes. Crystal structures of two of these inhibitors covalently bound to two different serine β-lactamases, class C Pseudomonas aeruginosa AmpC and class D OXA-10, are described herein. Improved physicochemical properties as well as increased activity against an array of β-lactamases resulted in substantial restoration of susceptibility to ceftazidime in Escherichia coli and Klebsiella pneumoniae.


    Organizational Affiliation

    Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham Massachusetts 02451, United States.




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 3 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
3VT
Query on 3VT

Download SDF File 
Download CCD File 
A
[(3R)-1-hydroxy-4,5-dimethyl-6-(pyrazin-2-yloxy)-1,3-dihydro-2,1-benzoxaborol-3-yl]acetic acid
C15 H15 B N2 O5
MTHDAYXINWUJNY-GFCCVEGCSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.745α = 90.00
b = 70.824β = 90.00
c = 106.230γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
Aimlessdata scaling
BUSTERrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-18 
  • Released Date: 2015-08-05 
  • Deposition Author(s): Ferguson, A.D.

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references, Derived calculations