6Q7V

Crystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Flexible Fragment Growing Boosts Potency of Quorum-Sensing Inhibitors against Pseudomonas aeruginosa Virulence.

Zender, M.Witzgall, F.Kiefer, A.Kirsch, B.Maurer, C.K.Kany, A.M.Xu, N.Schmelz, S.Borger, C.Blankenfeldt, W.Empting, M.

(2020) ChemMedChem 15: 188-194

  • DOI: https://doi.org/10.1002/cmdc.201900621
  • Primary Citation of Related Structures:  
    6Q7U, 6Q7V, 6Q7W

  • PubMed Abstract: 

    Hit-to-lead optimization is a critical phase in drug discovery. Herein, we report on the fragment-based discovery and optimization of 2-aminopyridine derivatives as a novel lead-like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa. We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal (PQS) quorum sensing (QS) system leading to an abolishment of bacterial pathogenicity. Our compounds act on the PQS receptor (PqsR), a key transcription factor controlling the expression of various pathogenicity determinants. In this target-driven approach, we made use of biophysical screening via surface plasmon resonance (SPR) followed by isothermal titration calorimetry (ITC)-enabled enthalpic efficiency (EE) evaluation. Hit optimization then involved growth vector identification and exploitation. Astonishingly, the latter was successfully achieved by introducing flexible linkers rather than rigid motifs leading to a boost in activity on the target receptor and anti-virulence potency.


  • Organizational Affiliation

    Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator MvfR
A, B
229Pseudomonas 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HLK
Query on HLK

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
~{N}4-[(4-fluorophenyl)methyl]-6-(trifluoromethyl)pyridine-2,4-diamine
C13 H11 F4 N3
NVURBNAAKDVJHE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.38α = 90
b = 119.31β = 90
c = 114.408γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description