High resolution crystal structure of N-terminal domain of PEX14 from Trypanosoma brucei in complex with the fist compound with sub-micromolar trypanocidal activity

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.111 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structure-Activity Relationship in Pyrazolo[4,3-c]pyridines, First Inhibitors of PEX14-PEX5 Protein-Protein Interaction with Trypanocidal Activity.

Dawidowski, M.Kalel, V.C.Napolitano, V.Fino, R.Schorpp, K.Emmanouilidis, L.Lenhart, D.Ostertag, M.Kaiser, M.Kolonko, M.Tippler, B.Schliebs, W.Dubin, G.Maser, P.Tetko, I.V.Hadian, K.Plettenburg, O.Erdmann, R.Sattler, M.Popowicz, G.M.

(2020) J Med Chem 63: 847-879

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01876
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Trypanosoma protists are pathogens leading to a spectrum of devastating infectious diseases. The range of available chemotherapeutics against Trypanosoma is limited, and the existing therapies are partially ineffective and cause serious adverse effects. Formation of the PEX14-PEX5 complex is essential for protein import into the parasites' glycosomes. This transport is critical for parasite metabolism and failure leads to mislocalization of glycosomal enzymes, with fatal consequences for the parasite. Hence, inhibiting the PEX14-PEX5 protein-protein interaction (PPI) is an attractive way to affect multiple metabolic pathways. Herein, we have used structure-guided computational screening and optimization to develop the first line of compounds that inhibit PEX14-PEX5 PPI. The optimization was driven by several X-ray structures, NMR binding data, and molecular dynamics simulations. Importantly, the developed compounds show significant cellular activity against Trypanosoma , including the human pathogen Trypanosoma brucei gambiense and Trypanosoma cruzi parasites.

  • Organizational Affiliation

    Center for Integrated Protein Science Munich at Chair of Biomolecular NMR, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxin 1469Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PEX14
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FTW (Subject of Investigation/LOI)
Query on FTW

Download Ideal Coordinates CCD File 
B [auth A]5-[(4-methoxynaphthalen-1-yl)methyl]-1-[2-[(2-methyl-1-oxidanyl-propan-2-yl)amino]ethyl]-~{N}-(naphthalen-1-ylmethyl)-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide
C36 H41 N5 O3
Query on BME

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
C2 H6 O S
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.111 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.935α = 90
b = 45.935β = 90
c = 63.733γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Accelerated Early staGe drug dIScoveryGermany675555

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references