8Q5K

PqsR coinducer binding domain of Pseudomonas aeruginosa with ligand 2t : 2-(4-(3-((6-chloro-1-(2-methoxyethyl)-1H-benzo[d]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis, and Evaluation of New 1 H -Benzo[ d ]imidazole Based PqsR Inhibitors as Adjuvant Therapy for Pseudomonas aeruginosa Infections.

Soukarieh, F.Mashabi, A.Richardson, W.Oton, E.V.Romero, M.Dubern, J.F.Robertson, S.N.Lucanto, S.Markham-Lee, Z.Sou, T.Kukavica-Ibrulj, I.Levesque, R.C.Bergstrom, C.A.S.Halliday, N.Kellam, B.Emsley, J.Heeb, S.Williams, P.Stocks, M.J.Camara, M.

(2024) J Med Chem 67: 1008-1023

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00973
  • Primary Citation of Related Structures:  
    8Q5K, 8Q5L

  • PubMed Abstract: 

    Pseudomonas aeruginosa is one of the top priority pathogens that requires immediate attention according to the World Health Organisation (WHO). Due to the alarming shortage of novel antimicrobials, targeting quorum sensing (QS), a bacterial cell to cell signaling system controlling virulence, has emerged as a promising approach as an antibiotic adjuvant therapy. Interference with the pqs system, one of three QS systems in P. aeruginosa , results in reduction of bacterial virulence gene expression and biofilm maturation. Herein, we report a hit to lead process to fine-tune the potency of our previously reported inhibitor 1 (IC 50 3.2 μM in P. aeruginosa PAO1-L), which led to the discovery of 2-(4-(3-((6-chloro-1-isopropyl-1 H -benzo[ d ]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile ( 6f ) as a potent PqsR antagonist. Compound 6f inhibited the PqsR-controlled P pqsA - lux transcriptional reporter fusion in P. aeruginosa at low submicromolar concentrations. Moreover, 6f showed improved efficacy against P. aeruginosa CF isolates with significant inhibition of pyocyanin, 2-alkyl-4(1 H )-quinolones production.


  • Organizational Affiliation

    School of Life Sciences, University of Nottingham Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multiple virulence factor regulator MvfR216Pseudomonas aeruginosa UCBPP-PA14Mutation(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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JTI (Subject of Investigation/LOI)
Query on JTI

Download Ideal Coordinates CCD File 
B [auth A]2-[4-[(2~{S})-3-[[6-chloranyl-1-(2-methoxyethyl)benzimidazol-2-yl]amino]-2-oxidanyl-propoxy]phenyl]ethanenitrile
C21 H23 Cl N4 O3
MZCRDZUXHLAMCH-KRWDZBQOSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.033α = 90
b = 119.033β = 90
c = 115.919γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/N006615/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/K005138/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/N03371X/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/ N501852/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R012415/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X002950/1
Wellcome TrustUnited Kingdom108876/B/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references
  • Version 1.2: 2024-04-17
    Changes: Database references, Source and taxonomy, Structure summary