9F8R | pdb_00009f8r

Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (4-Chlorophenyl)[2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

From Bones to Bugs: Structure-Based Development of Raloxifene-Derived Pathoblockers That Inhibit Pyocyanin Production in Pseudomonas aeruginosa.

Thiemann, M.Zimmermann, M.Diederich, C.Zhan, H.Lebedev, M.Pletz, J.Baumgarten, J.Handke, M.Musken, M.Breinbauer, R.Krasteva-Christ, G.Zanin, E.Empting, M.Schiedel, M.Kunick, C.Blankenfeldt, W.

(2025) J Med Chem 68: 7390-7420

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c03065
  • Primary Citation Related Structures: 
    9F8H, 9F8I, 9F8J, 9F8K, 9F8L, 9F8M, 9F8N, 9F8O, 9F8P, 9F8Q, 9F8R, 9F8S

  • PubMed Abstract: 

    The human pathogen Pseudomonas aeruginosa is particularly notorious for its multiple resistance mechanisms. A new concept for anti-infectives is the "pathoblocker" approach, which targets virulence factors to disarm rather than kill pathogens and thus attenuates the development of resistance. Based on the estrogen receptor modulator raloxifene, which had previously been identified as a potential biosynthesis inhibitor of the virulence factor pyocyanin via in silico screening, analogues have been developed as pathoblockers against P. aeruginosa . These compounds reduce the production of pyocyanin by binding to the phenazine biosynthesis enzyme PhzB. Structure-activity relationships (SAR) were explored using nano differential scanning fluorimetry, isothermal titration calorimetry, and 12 X-ray cocrystal structures. Compared to raloxifene, congener 20c shows a 60-fold lower affinity for the human estrogen receptor with a 15-fold increase in pyocyanin inhibitory activity. The comprehensive structural information gathered in this study paves the way for the development of improved pathoblockers with increased potency and selectivity.


  • Organizational Affiliation
    • Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 88.61 kDa 
  • Atom Count: 5,741 
  • Modeled Residue Count: 612 
  • Deposited Residue Count: 740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phenazine biosynthesis protein A/B
A, B, C, D
185Burkholderia lataMutation(s): 0 
Gene Names: Bcep18194_B1568
UniProt
Find proteins for Q396C9 (Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383))
Explore Q396C9 
Go to UniProtKB:  Q396C9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ396C9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IAN
(Subject of Investigation/LOI)

Query on A1IAN



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
M [auth C],
O [auth D]
(4-chlorophenyl)-[2-(4-hydroxyphenyl)-1-benzothiophen-3-yl]methanone
C21 H13 Cl O2 S
HTZYRZQECOXVQX-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
J [auth C],
N [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
K [auth C],
L [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
P [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.217 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.933α = 90
b = 69.015β = 90.13
c = 83.35γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
autoPROCdata processing
PDB_EXTRACTdata extraction

Structure Validation

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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: 2025-04-16
    Type: Initial release