5FGZ

E. coli PBP1b in complex with FPI-1465


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Kinetic Characterization of Diazabicyclooctanes as Dual Inhibitors of Both Serine-beta-Lactamases and Penicillin-Binding Proteins.

King, A.M.King, D.T.French, S.Brouillette, E.Asli, A.Alexander, J.A.Vuckovic, M.Maiti, S.N.Parr, T.R.Brown, E.D.Malouin, F.Strynadka, N.C.Wright, G.D.

(2016) ACS Chem Biol 11: 864-868

  • DOI: 10.1021/acschembio.5b00944
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Avibactam is a diazabicyclooctane β-lactamase inhibitor possessing outstanding but incomplete efficacy against multidrug-resistant Gram-negative pathogens in combination with β-lactam antibiotics. Significant pharmaceutical investment in generating d ...

    Avibactam is a diazabicyclooctane β-lactamase inhibitor possessing outstanding but incomplete efficacy against multidrug-resistant Gram-negative pathogens in combination with β-lactam antibiotics. Significant pharmaceutical investment in generating derivatives of avibactam warrants a thorough characterization of their activity. We show here through structural and kinetic analysis that select diazabicyclooctane derivatives display effective but varied inhibition of two clinically important β-lactamases (CTX-M-15 and OXA-48). Furthermore, these derivatives exhibit considerable antimicrobial activity (MIC ≤ 2 μg/mL) against clinical isolates of Pseudomonas aeruginosa, Escherichia coli, and Enterobacter spp. Imaging of cell phenotype along with structural and biochemical experiments unambiguously demonstrate that this activity, in E. coli, is a result of targeting penicillin-binding protein 2. Our results suggest that structure-activity relationship studies for the purpose of drug discovery must consider both β-lactamases and penicillin-binding proteins as targets. We believe that this approach will yield next-generation combination or monotherapies with an expanded spectrum of activity against currently untreatable Gram-negative pathogens.


    Organizational Affiliation

    M.G. DeGroote Institute for Infectious Disease Research, McMaster University , Hamilton, Ontario L8S 4K1, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 1B
A
747Escherichia coli K-12Mutation(s): 0 
Gene Names: mrcBpbpFponBb0149JW0145
EC: 2.4.1.129 (PDB Primary Data), 3.4 (PDB Primary Data), 3.4.16.4 (UniProt)
Find proteins for P02919 (Escherichia coli (strain K12))
Go to UniProtKB:  P02919
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0E
Query on M0E

Download CCD File 
A
MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N
 Ligand Interaction
5VW
Query on 5VW

Download CCD File 
A
[[(3~{R},6~{S})-1-methanoyl-6-[[(3~{S})-pyrrolidin-3-yl]oxycarbamoyl]piperidin-3-yl]amino] hydrogen sulfate
C11 H20 N4 O7 S
RTYOMSYVLRQWIH-UTLUCORTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.48α = 90
b = 63.22β = 90
c = 293.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Canadian Foundation for InnovationCanada--
Canada Research Chair ProgramsCanada--
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence