6OEZ | pdb_00006oez

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor (+)-N-(Cyclobutylmethyl)-3-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-2-(1-{[(2S)-pyrro-lidin-2-yl]methyl}-1H-indol-5-yl)-1,3-thiazol-4-yl}prop-2-yn-1-amine

• PDB DOI: https://doi.org/10.2210/pdb6OEZ/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-03-28 Released: 2019-07-31 
• Deposition Author(s): Halgas, O., De Gasparo, R., Harangozo, D., Krauth-Siegel, R.L., Diederich, F., Pai, E.F.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Targeting a Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase.

De Gasparo, R., Halgas, O., Harangozo, D., Kaiser, M., Pai, E.F., Krauth-Siegel, R.L., Diederich, F.

(2019) Chemistry 25: 11416-11421

• PubMed: 31407832 
• DOI: https://doi.org/10.1002/chem.201901664
• Primary Citation Related Structures: 
  6OEX, 6OEY, 6OEZ


• PubMed Abstract: 
  

  Trypanothione reductase (TR) plays a key role in the unique redox metabolism of trypanosomatids, the causative agents of human African trypanosomiasis (HAT), Chagas' disease, and leishmaniases. Introduction of a new, lean propargylic vector to a known class of TR inhibitors resulted in the strongest reported competitive inhibitor of Trypanosoma (T.) brucei TR, with an inhibition constant K _i of 73 nm, which is fully selective against human glutathione reductase (hGR). The best ligands exhibited in vitro IC ₅₀ values (half-maximal inhibitory concentration) against the HAT pathogen, T. brucei rhodesiense, in the mid-nanomolar range, reaching down to 50 nm. X-Ray co-crystal structures confirmed the binding mode of the ligands and revealed the presence of a HEPES buffer molecule in the large active site. Extension of the propargylic vector, guided by structure-based design, to replace the HEPES buffer molecule should give inhibitors with low nanomolar K _i and IC ₅₀ values for in vivo studies.

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Organizational Affiliation: 
• Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
Departments of Biochemistry and Medical Biophysics, University of Toronto, Medical Sciences Building, 5318, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
The Campbell Family Institute for Cancer Research, University Health Network, 101 College Street, Toronto, ON, M5G 1L7, Canada.
Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.
University of Basel, Petersplatz 1, 4003, Basel, Switzerland.
Biochemie-Zentrum Heidelberg (BZH), Universität Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 110.16 kDa 
• Atom Count: 7,795 
• Modeled Residue Count: 971 
• Deposited Residue Count: 990 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypanothione reductase	A [auth B], B [auth A]	495	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb10.406.0520 EC: 1.8.1.12
UniProt
Find proteins for Q389T8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q389T8  Go to UniProtKB:  Q389T8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth B], F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
M9J	E [auth B], H [auth A]	N-(cyclobutylmethyl)-3-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-2-(1-{[(2S)-pyrrolidin-2-yl]methyl}-1H-indol-5-yl)-1,3-thiazol-4-yl}prop-2-yn-1-amine C34 H45 N5 S FHCOGWJRKLTMNQ-LJAQVGFWSA-N
EPE	D [auth B], G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.235 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.526	α = 90
b = 117.526	β = 90
c = 224.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-31 
Deposition Author(s): Halgas, O., De Gasparo, R., Harangozo, D., Krauth-Siegel, R.L., Diederich, F., Pai, E.F.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2015-04877

Revision History  

• Version 1.0: 2019-07-31
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2019-09-11
  Changes: Data collection, Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary