7NBW

Crystal structure of PqsR (MvfR) ligand-binding domain in complex with a pyridin agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Divergent synthesis and biological evaluation of 2-(trifluoromethyl)pyridines as virulence-attenuating inverse agonists targeting PqsR.

Schutz, C.Hodzic, A.Hamed, M.Abdelsamie, A.S.Kany, A.M.Bauer, M.Rohrig, T.Schmelz, S.Scrima, A.Blankenfeldt, W.Empting, M.

(2021) Eur J Med Chem 226: 113797-113797

  • DOI: https://doi.org/10.1016/j.ejmech.2021.113797
  • Primary Citation of Related Structures:  
    7NBW

  • PubMed Abstract: 

    A short and divergent route towards new derivatives of 2-(trifluoromethyl)pyridines as potent inverse agonists of the bacterial target PqsR against Pseudomonas aeruginosa (PA) infections is described. This Gram-negative pathogen causes severe nosocomial infections and common antibiotic treatment options are rendered ineffective due to resistance issues. Based on an earlier identified optimized hit, we conducted derivatization and rigidification attempts employing two central building blocks. The western part of the molecule is built up via a 2-(trifluoromethyl)pyridine head group equipped with a terminal alkyne. The eastern section is then introduced through aryliode motifs exploiting Sonogashira as well as Suzuki-type chemistry. Subsequent modification provided quick access to an array of compounds, allowed for deep SAR insights, and enabled to optimize the hit scaffold into a lead structure of nanomolar potency combined with favorable in vitro ADME/T features.


  • Organizational Affiliation

    Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator MvfR229Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: mvfRPA1003
UniProt
Find proteins for Q9I4X0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4X0 
Go to UniProtKB:  Q9I4X0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4X0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U7Q (Subject of Investigation/LOI)
Query on U7Q

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[3-(4-fluorophenyl)prop-2-ynyl]-2-(trifluoromethyl)pyridin-4-amine
C15 H10 F4 N2
LOCKKGFITVJYKW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.386α = 90
b = 121.386β = 90
c = 114.839γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata 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: 2021-10-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description