6G9F

Structural basis for the inhibition of E. coli PBP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.

Levy, N.Bruneau, J.M.Le Rouzic, E.Bonnard, D.Le Strat, F.Caravano, A.Chevreuil, F.Barbion, J.Chasset, S.Ledoussal, B.Moreau, F.Ruff, M.

(2019) J.Med.Chem. 62: 4742-4754

  • DOI: 10.1021/acs.jmedchem.9b00338
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Penicillin-binding proteins (PBPs) are the targets of the β-lactams, the most successful class of antibiotics ever developed against bacterial infections. Unfortunately, the worldwide and rapid spread of large spectrum β-lactam resistance genes such ...

    Penicillin-binding proteins (PBPs) are the targets of the β-lactams, the most successful class of antibiotics ever developed against bacterial infections. Unfortunately, the worldwide and rapid spread of large spectrum β-lactam resistance genes such as carbapenemases is detrimental to the use of antibiotics in this class. New potent PBP inhibitors are needed, especially compounds that resist β-lactamase hydrolysis. Here we describe the structure of the E. coli PBP2 in its Apo form and upon its reaction with 2 diazabicyclo derivatives, avibactam and CPD4, a new potent PBP2 inhibitor. Examination of these structures shows that unlike avibactam, CPD4 can perform a hydrophobic stacking on Trp370 in the active site of E. coli PBP2. This result, together with sequence analysis, homology modeling, and SAR, allows us to propose CPD4 as potential starting scaffold to develop molecules active against a broad range of bacterial species at the top of the WHO priority list.


    Organizational Affiliation

    Mutabilis , 102 Avenue Gaston Roussel , 93230 Romainville , France.,IGBMC , 1 Rue Laurent Fries , 67404 Illkirch , France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan D,D-transpeptidase MrdA
A
561Escherichia coli O157:H7Mutation(s): 0 
Gene Names: mrdA (pbpA)
EC: 3.4.16.4
Find proteins for P0AD67 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AD67
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NXL
Query on NXL

Download SDF File 
Download CCD File 
A
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
avibactam, bound form, NXL104, bound form
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 125.078α = 90.00
b = 182.875β = 90.00
c = 74.767γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-10 
  • Released Date: 2019-05-22 
  • Deposition Author(s): Ruff, M., Levy, N.

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release