6I30

Crystal structure of the AmpC from Pseudomonas aeruginosa with 1C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Studies on the inhibition of AmpC and other beta-lactamases by cyclic boronates.

Cahill, S.T.Tyrrell, J.M.Navratilova, I.H.Calvopina, K.Robinson, S.W.Lohans, C.T.McDonough, M.A.Cain, R.Fishwick, C.W.G.Avison, M.B.Walsh, T.R.Schofield, C.J.Brem, J.

(2019) Biochim Biophys Acta Gen Subj 1863: 742-748

  • DOI: https://doi.org/10.1016/j.bbagen.2019.02.004
  • Primary Citation of Related Structures:  
    6I30

  • PubMed Abstract: 

    The β-lactam antibiotics represent the most successful drug class for treatment of bacterial infections. Resistance to them, importantly via production of β-lactamases, which collectively are able to hydrolyse all classes of β-lactams, threatens their continued widespread use. Bicyclic boronates show potential as broad spectrum inhibitors of the mechanistically distinct serine- (SBL) and metallo- (MBL) β-lactamase families. Using biophysical methods, including crystallographic analysis, we have investigated the binding mode of bicyclic boronates to clinically important β-lactamases. Induction experiments and agar-based MIC screening against MDR-Enterobacteriaceae (n = 132) were used to evaluate induction properties and the in vitro efficacy of a bicyclic boronate in combination with meropenem. Crystallographic analysis of a bicyclic boronate in complex with AmpC from Pseudomonas aeruginosa reveals it binds to form a tetrahedral boronate species. Microbiological studies on the clinical coverage (in combination with meropenem) and induction of β-lactamases by bicyclic boronates further support the promise of such compounds as broad spectrum β-lactamase inhibitors. Together with reported studies on the structural basis of their inhibition of class A, B and D β-lactamases, biophysical studies, including crystallographic analysis, support the proposal that bicyclic boronates mimic tetrahedral intermediates common to SBL and MBL catalysis. Bicyclic boronates are a new generation of broad spectrum inhibitors of both SBLs and MBLs.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Class C beta-lactamase PDC-301358Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaPDC
EC: 3.5.2.6
UniProt
Find proteins for A0A2Z4BUZ1 (Pseudomonas aeruginosa)
Explore A0A2Z4BUZ1 
Go to UniProtKB:  A0A2Z4BUZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z4BUZ1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C6S
Query on C6S

Download Ideal Coordinates CCD File 
B [auth A](3R)-3-(cyclohexylcarbonylamino)-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
C16 H20 B N O5
ZRHUJXRVIMMHFG-ZDUSSCGKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.04α = 90
b = 75.34β = 90
c = 100.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary