9FQY | pdb_00009fqy

Pseudomonas aeruginosa Elastase in complex with a phosphonate based inhibitor (R-configured)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.184 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dipeptidic Phosphonates: Potent Inhibitors of Pseudomonas aeruginosa Elastase B Showing Efficacy in a Murine Keratitis Model.

Kiefer, A.F.Schutz, C.Englisch, C.N.Kolling, D.Speicher, S.Kany, A.M.Shafiei, R.Wadood, N.A.Aljohmani, A.Wirschem, N.Jumde, R.P.Klein, A.Sikandar, A.Park, Y.M.Krasteva-Christ, G.Yildiz, D.Abdelsamie, A.S.Rox, K.Kohnke, J.Muller, R.Bischoff, M.Haupenthal, J.Hirsch, A.K.H.

(2025) Adv Sci (Weinh) 12: e2411807-e2411807

  • DOI: https://doi.org/10.1002/advs.202411807
  • Primary Citation of Related Structures:  
    8R1B, 9FQD, 9FQY

  • PubMed Abstract: 

    The ubiquitous opportunistic pathogen Pseudomonas aeruginosa is responsible for severe infections and notoriously known for acquiring antimicrobial resistance. Inhibiting the bacterium's extracellular elastase, LasB - a zinc-dependent protease - presents a promising strategy to mitigate its virulence. Within this medicinal chemistry-driven hit-to-lead optimization campaign, a new series of highly potent dipeptidic phosphonates is designed and synthesized following a structure-based drug-discovery approach. In vitro and in vivo evaluation reveal beneficial pharmacokinetic profiles, excellent selectivity over human off-targets and good tolerability in murine toxicity studies. Ultimately, the scaffold presented herein demonstrates promising in vivo efficacy in a murine Pseudomonas aeruginosa keratitis model in combination with the antibiotic meropenem.


  • Organizational Affiliation
    • Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Campus E8.1, 66123, Saarbrücken, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elastase301Pseudomonas aeruginosaMutation(s): 0 
EC: 3.4.24.26
UniProt
Find proteins for P14756 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P14756 
Go to UniProtKB:  P14756
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14756
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IFN (Subject of Investigation/LOI)
Query on A1IFN

Download Ideal Coordinates CCD File 
D [auth A][(2~{R})-4-methyl-1-[[(2~{S})-3-methyl-1-oxidanylidene-1-[[4-[2,2,2-tris(fluoranyl)ethanoyl]phenyl]amino]butan-2-yl]amino]-1-oxidanylidene-pentan-2-yl]phosphonic acid
C19 H26 F3 N2 O6 P
GKDUMYHHGNKYPT-CABCVRRESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.184 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.613α = 90
b = 51.323β = 90
c = 120.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references