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 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acsinfecdis.5b00031
  • Primary Citation of Related Structures:  
    4WYY, 4WZ4, 4WZ5

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase360Pseudomonas 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VT
Query on 3VT

Download Ideal Coordinates CCD File 
G [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.745α = 90
b = 70.824β = 90
c = 106.23γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary