5DCH

Crystal structure of Pseudomonas aeruginosa DsbA E82I in complex with MIPS-0000851 (3-[(2-METHYLBENZYL)SULFANYL]-4H-1,2,4-TRIAZOL-4-AMINE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.447 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment library screening identifies hits that bind to the non-catalytic surface of Pseudomonas aeruginosa DsbA1.

Mohanty, B.Rimmer, K.McMahon, R.M.Headey, S.J.Vazirani, M.Shouldice, S.R.Coincon, M.Tay, S.Morton, C.J.Simpson, J.S.Martin, J.L.Scanlon, M.J.

(2017) PLoS ONE 12: e0173436-e0173436

  • DOI: 10.1371/journal.pone.0173436
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • At a time when the antibiotic drug discovery pipeline has stalled, antibiotic resistance is accelerating with catastrophic implications for our ability to treat bacterial infections. Globally we face the prospect of a future when common infections ca ...

    At a time when the antibiotic drug discovery pipeline has stalled, antibiotic resistance is accelerating with catastrophic implications for our ability to treat bacterial infections. Globally we face the prospect of a future when common infections can once again kill. Anti-virulence approaches that target the capacity of the bacterium to cause disease rather than the growth or survival of the bacterium itself offer a tantalizing prospect of novel antimicrobials. They may also reduce the propensity to induce resistance by removing the strong selection pressure imparted by bactericidal or bacteriostatic agents. In the human pathogen Pseudomonas aeruginosa, disulfide bond protein A (PaDsbA1) plays a central role in the oxidative folding of virulence factors and is therefore an attractive target for the development of new anti-virulence antimicrobials. Using a fragment-based approach we have identified small molecules that bind to PaDsbA1. The fragment hits show selective binding to PaDsbA1 over the DsbA protein from Escherichia coli, suggesting that developing species-specific narrow-spectrum inhibitors of DsbA enzymes may be feasible. Structures of a co-complex of PaDsbA1 with the highest affinity fragment identified in the screen reveal that the fragment binds on the non-catalytic surface of the protein at a domain interface. This biophysical and structural data represent a starting point in the development of higher affinity compounds, which will be assessed for their potential as selective PaDsbA1 inhibitors.


    Organizational Affiliation

    Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.,The University of Queensland, Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, Brisbane, Queensland, Australia.,Biota Holdings Limited, Notting Hill, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein DsbA
A
192Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Gene Names: dsbA
Find proteins for P0C2B2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P0C2B2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
1YO
Query on 1YO

Download SDF File 
Download CCD File 
A
3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine
C10 H12 N4 S
UVAUEHMNFBWZNL-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.447 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.470α = 90.00
b = 63.100β = 98.31
c = 41.870γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research CouncilAustraliaLP0990166
Australian Research CouncilAustraliaFL0992138

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references