Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.94 kDa 
• Atom Count: 1622 
• Modelled Residue Count: 204 
• Deposited Residue Count: 229 
• Unique protein chains: 1

6Q7U

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

• DOI: 10.2210/pdb6Q7U/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-13 Released: 2019-11-20 
• Deposition Author(s): Witzgall, F., Xu, N., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

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

• PubMed: 31709767 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator MvfR	A	229	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: mvfR, PA1003
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HLH (Subject of Investigation/LOI)	B [auth A]	2-heptyl-1~{H}-quinolin-4-one C16 H21 N O UYRHHBXYXSYGHA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.271 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.592	α = 90
b = 116.592	β = 90
c = 115.328	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2018-12-13 
• Released Date: 2019-11-20 
Deposition Author(s): Witzgall, F., Xu, N., Blankenfeldt, W.

Revision History  

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