8R1B | pdb_00008r1b

Crystal structure of recombinant LasB from Pseudomonas aeruginosa PAO1 in complex with 6466


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 
    0.167 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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) : e2411807-e2411807

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

  • 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
Pro-elastase514Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lasBPA3724
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XI5 (Subject of Investigation/LOI)
Query on XI5

Download Ideal Coordinates CCD File 
H [auth A][(2~{S})-1-[[1-[(4-ethanoylphenyl)amino]-3-methyl-1-oxidanylidene-butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]phosphonic acid
C19 H29 N2 O6 P
NDYKWZBIJQYUHB-IRXDYDNUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
G [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
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: 1.31 Å
  • R-Value Free:  0.167 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.144 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.372α = 90
b = 89.982β = 114.085
c = 40.826γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted XI5Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references