5N8V

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

PDB DOI: https://doi.org/10.2210/pdb5N8V/pdb

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

Deposited: 2017-02-24 Released: 2017-03-15
Deposition Author(s): Dawidowski, M., Emmanouilidis, L., Sattler, M., Popowicz, G.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.217
R-Value Work: 0.195
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 28360328 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 34.57 kDa
Atom Count: 2,434
Modelled Residue Count: 252
Deposited Residue Count: 276
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A, B, C [auth D], D [auth F]	69	Trypanosoma brucei brucei	Mutation(s): 0 Gene Names: PEX14
UniProt
Find proteins for Q8IEW2 (Trypanosoma brucei brucei) Explore Q8IEW2 Go to UniProtKB: Q8IEW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IEW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KZZ Query on KZZ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain S [auth F] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain S [auth F]	E [auth A], K [auth B], O [auth D], S [auth F]	1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide C₃₂ H₃₃ N₅ O₂ WADXPVUOGGMXPD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth F] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D]	F [auth A] G [auth A] H [auth A] L [auth B] P [auth D] F [auth A], G [auth A], H [auth A], L [auth B], P [auth D], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth D] Focus chain Q [auth D]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth D] SDF format, chain T [auth F] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth F]	I [auth A], M [auth B], R [auth D], T [auth F]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth D] Focus chain T [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B]	J [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]