5L87

Targeting the PEX14-PEX5 interaction by small molecules provides novel therapeutic routes to treat trypanosomiases.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Inhibitors of PEX14 disrupt protein import into glycosomes and kill Trypanosoma parasites.

Dawidowski, M.Emmanouilidis, L.Kalel, V.C.Tripsianes, K.Schorpp, K.Hadian, K.Kaiser, M.Maser, P.Kolonko, M.Tanghe, S.Rodriguez, A.Schliebs, W.Erdmann, R.Sattler, M.Popowicz, G.M.

(2017) Science 355: 1416-1420

  • DOI: https://doi.org/10.1126/science.aal1807
  • Primary Citation of Related Structures:  
    5L87, 5L8A, 5MMC, 5N8V

  • PubMed Abstract: 

    The parasitic protists of the Trypanosoma genus infect humans and domestic mammals, causing severe mortality and huge economic losses. The most threatening trypanosomiasis is Chagas disease, affecting up to 12 million people in the Americas. We report a way to selectively kill Trypanosoma by blocking glycosomal/peroxisomal import that depends on the PEX14-PEX5 protein-protein interaction. We developed small molecules that efficiently disrupt the PEX14-PEX5 interaction. This results in mislocalization of glycosomal enzymes, causing metabolic catastrophe, and it kills the parasite. High-resolution x-ray structures and nuclear magnetic resonance data enabled the efficient design of inhibitors with trypanocidal activities comparable to approved medications. These results identify PEX14 as an "Achilles' heel" of the Trypanosoma suitable for the development of new therapies against trypanosomiases and provide the structural basis for their development.


  • Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin 1469Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PEX14
UniProt
Find proteins for Q8IEW2 (Trypanosoma brucei brucei)
Explore Q8IEW2 
Go to UniProtKB:  Q8IEW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IEW2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6RD
Query on 6RD

Download Ideal Coordinates CCD File 
B [auth A]5-(1~{H}-indol-3-ylmethyl)-1-methyl-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide
C28 H27 N5 O
XJVZXIUKPNWOSD-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6RD Binding MOAD:  5L87 Ki: 8430 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.130 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.03α = 90
b = 37.26β = 117.89
c = 42.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1905 ER178/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description