7JWL

Crystal Structure of Pseudomonas aeruginosa Penicillin Binding Protein 3 (PAE-PBP3) bound to ETX0462


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Rational design of a new antibiotic class for drug-resistant infections.

Durand-Reville, T.F.Miller, A.A.O'Donnell, J.P.Wu, X.Sylvester, M.A.Guler, S.Iyer, R.Shapiro, A.B.Carter, N.M.Velez-Vega, C.Moussa, S.H.McLeod, S.M.Chen, A.Tanudra, A.M.Zhang, J.Comita-Prevoir, J.Romero, J.A.Huynh, H.Ferguson, A.D.Horanyi, P.S.Mayclin, S.J.Heine, H.S.Drusano, G.L.Cummings, J.E.Slayden, R.A.Tommasi, R.A.

(2021) Nature 597: 698-702

  • DOI: https://doi.org/10.1038/s41586-021-03899-0
  • Primary Citation of Related Structures:  
    7JWL

  • PubMed Abstract: 

    The development of new antibiotics to treat infections caused by drug-resistant Gram-negative pathogens is of paramount importance as antibiotic resistance continues to increase worldwide 1 . Here we describe a strategy for the rational design of diazabicyclooctane inhibitors of penicillin-binding proteins from Gram-negative bacteria to overcome multiple mechanisms of resistance, including β-lactamase enzymes, stringent response and outer membrane permeation. Diazabicyclooctane inhibitors retain activity in the presence of β-lactamases, the primary resistance mechanism associated with β-lactam therapy in Gram-negative bacteria 2,3 . Although the target spectrum of an initial lead was successfully re-engineered to gain in vivo efficacy, its ability to permeate across bacterial outer membranes was insufficient for further development. Notably, the features that enhanced target potency were found to preclude compound uptake. An improved optimization strategy leveraged porin permeation properties concomitant with biochemical potency in the lead-optimization stage. This resulted in ETX0462, which has potent in vitro and in vivo activity against Pseudomonas aeruginosa plus all other Gram-negative ESKAPE pathogens, Stenotrophomonas maltophilia and biothreat pathogens. These attributes, along with a favourable preclinical safety profile, hold promise for the successful clinical development of the first novel Gram-negative chemotype to treat life-threatening antibiotic-resistant infections in more than 25 years.


  • Organizational Affiliation

    Entasis Therapeutics, Waltham, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan D,D-transpeptidase FtsI538Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
EC: 3.4.16.4
UniProt
Find proteins for G3XD46 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD46 
Go to UniProtKB:  G3XD46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD46
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.54α = 90
b = 83.95β = 90
c = 90.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Database references
  • Version 1.2: 2021-09-22
    Changes: Database references
  • Version 1.3: 2021-09-29
    Changes: Database references
  • Version 1.4: 2021-10-13
    Changes: Database references
  • Version 1.5: 2023-10-18
    Changes: Data collection, Refinement description