5L8A | pdb_00005l8a

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

• PDB DOI: https://doi.org/10.2210/pdb5L8A/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-07 Released: 2017-03-08 
• Deposition Author(s): Dawidowski, M., Emmanouilidis, L., Sattler, M., Popowicz, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.252 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 28360328 
• DOI: https://doi.org/10.1126/science.aal1807
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany.
Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany.
CEITEC, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland.
University of Basel, 4001 Basel, Switzerland.
New York University School of Medicine, Department of Microbiology, 341 East 25th Street, Room 513, New York, NY 10010, USA.
Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr University Bochum, 44780 Bochum, Germany. [e-mail] [e-mail] [e-mail].
Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.57 kDa 
• Atom Count: 2,370 
• Modeled Residue Count: 248 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A, B, C, D	69	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: PEX14
UniProt
Find proteins for Q8IEW2 (Trypanosoma brucei brucei) Explore Q8IEW2  Go to UniProtKB:  Q8IEW2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RB	E [auth A], G [auth B], H [auth C], J [auth D]	1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-(phenylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide C28 H30 N4 O3 ZHTGDAFDEHXYSS-UHFFFAOYSA-N
GLY	F [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.252 (Depositor) 
• R-Value Work:  0.191 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.1	α = 94.12
b = 36.28	β = 105.87
c = 55.31	γ = 100.54

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Dawidowski, M., Emmanouilidis, L., Sattler, M., Popowicz, G.M.

Revision History  

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