9H0Y | pdb_00009h0y

ProA in complex with inhibitor 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.166 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9H0Y

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Innovative zinc-binding inhibitors of Legionella pneumophila ProA reduce collagen and flagellin degradation, TLR5 evasion, and human lung tissue inflammation.

Scheithauer, L.Ornago, C.Selmar, J.Schutz, C.Bianchi, G.Kiefer, A.Haupenthal, J.Dellmann, A.Huynh, D.Zhang, R.Blankenfeldt, W.Hirsch, A.H.Steinert, M.

(2025) Eur J Med Chem 296: 117832-117832

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117832
  • Primary Citation Related Structures: 
    9H0X, 9H0Y

  • PubMed Abstract: 

    Legionnaires' disease is a severe pneumonia caused by the aquatic bacterium Legionella pneumophila. In recent years, the number of cases has continuously increased according to the distribution of aerosol-producing technologies, global warming, and demographic ageing, which elevates bacterial transmission, environmental cell counts and host susceptibility. Despite the availability of an antibiotic therapy, this treatment cannot eradicate the risk of irreversible symptoms or high mortality rates. The bacterial zinc metalloprotease ProA significantly contributes to life-threatening tissue damage in patients and hence promotes progression of the disease. We hypothesize that additional application of an inhibitory agent against this protease may reduce serious complications and the risk of respiratory failure until successful bacterial clearance. Here we present a newly designed set of zinc-binding compounds and evaluated their inhibitory effects on the versatile physiological activity of ProA during infection. We identified a potent phosphonate inhibitor, which reduces ProA-dependent cleavage of host collagen IV and bacterial flagellin, immune evasion from the TLR5-NF-κB pathway and PMN-mediated inflammation in human lung tissue explants (HLTEs). Based on efficacy at the biochemical, cellular and tissue levels and the results of ProA co-crystallizations, we conclude that the selected inhibitors represent promising lead structures for the future development of clinically applicable pathoblockers against Legionnaires' disease.


  • Organizational Affiliation
    • Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 39.21 kDa 
  • Atom Count: 3,016 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 336 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc metalloproteinase336Legionella pneumophila str. CorbyMutation(s): 0 
EC: 3.4.24
UniProt
Find proteins for P21347 (Legionella pneumophila)
Explore P21347 
Go to UniProtKB:  P21347
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21347
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IRL
(Subject of Investigation/LOI)

Query on A1IRL



Download:Ideal Coordinates CCD File
B [auth A][(2~{R})-1-[[(2~{R})-1-[(3,4-dichlorophenyl)amino]-3-methyl-1-oxidanylidene-butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]phosphonic acid
C17 H25 Cl2 N2 O5 P
MGOFXJKMSWJECR-HUUCEWRRSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A],
M [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BU3

Query on BU3



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
F [auth A],
H [auth A],
I [auth A]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.166 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.65α = 90
b = 56.51β = 96.04
c = 74.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release