6PML

Crystal Structure of EcDsbA in complex benzyl ether 23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Fragment-Based Development of a Benzofuran Hit as a New Class ofEscherichia coliDsbA Inhibitors.

Duncan, L.F.Wang, G.Ilyichova, O.V.Scanlon, M.J.Heras, B.Abbott, B.M.

(2019) Molecules 24: --

  • DOI: 10.3390/molecules24203756
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A fragment-based drug discovery approach was taken to target the thiol-disulfide oxidoreductase enzyme DsbA from <i>Escherichia coli </i> ( <i>Ec </i>DsbA). This enzyme is critical for the correct folding of virulence factors in many pathogenic Gram ...

    A fragment-based drug discovery approach was taken to target the thiol-disulfide oxidoreductase enzyme DsbA from Escherichia coli ( Ec DsbA). This enzyme is critical for the correct folding of virulence factors in many pathogenic Gram-negative bacteria, and small molecule inhibitors can potentially be developed as anti-virulence compounds. Biophysical screening of a library of fragments identified several classes of fragments with affinity to Ec DsbA. One hit with high mM affinity, 2-(6-bromobenzofuran-3-yl)acetic acid ( 6 ), was chemically elaborated at several positions around the scaffold. X-ray crystal structures of the elaborated analogues showed binding in the hydrophobic binding groove adjacent to the catalytic disulfide bond of Ec DsbA. Binding affinity was calculated based on NMR studies and compounds 25 and 28 were identified as the highest affinity binders with dissociation constants ( K D ) of 326 ± 25 and 341 ± 57 µM respectively. This work suggests the potential to develop benzofuran fragments into a novel class of Ec DsbA inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia. G.Wang@latrobe.edu.au.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia. martin.scanlon@monash.edu.,ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia. martin.scanlon@monash.edu.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia. B.Abbott@latrobe.edu.au.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia. olga.illyichova@monash.edu.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia. B.Heras@latrobe.edu.au.,Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia. dunclf01@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein DsbA
A, B
189Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dsbA (dsf, ppfA)
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEG4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download SDF File 
Download CCD File 
B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
OR4
Query on OR4

Download SDF File 
Download CCD File 
A
[6-(benzyloxy)-1-benzofuran-3-yl]acetic acid
C17 H14 O4
VJEZHKLENQLLAZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.540α = 90.00
b = 63.740β = 140.85
c = 96.190γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release