6Q7W

Crystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1002/cmdc.201900621
  • Primary Citation of Related Structures:  
    6Q7U, 6Q7W, 6Q7V

  • 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 ...

    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

    Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator MvfRA229Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: mvfRPA1003
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HLQ
Query on HLQ

Download Ideal Coordinates CCD File 
A
~{N}4-[3-(4-fluorophenyl)propyl]-6-(trifluoromethyl)pyridine-2,4-diamine
C15 H15 F4 N3
AUZFKJZRALGBMB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.218α = 90
b = 121.218β = 90
c = 114.555γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references