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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/acschembio.5b00944
  • Primary Citation of Related Structures:  
    5FA7, 5FAO, 5FAP, 5FAQ, 5FAS, 5FAT, 5FGZ

  • 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 derivatives of avibactam warrants a thorough characterization of their activity ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein 1B747Escherichia coli K-12Mutation(s): 0 
Gene Names: mrcB, pbpF, ponB, b0149, JW0145
EC: 2.4.1.129 (PDB Primary Data), 3.4 (PDB Primary Data), 3.4.16.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P02919 (Escherichia coli (strain K12))
Explore P02919 
Go to UniProtKB:  P02919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02919
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0E
Query on M0E
Download Ideal Coordinates CCD File 
B [auth A]MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N		 Ligand Interaction
5VW
Query on 5VW
Download Ideal Coordinates CCD File 
C [auth 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

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • 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