6OEX

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor 3-(2-{1-[2-(Piperidin-4-yl)ethyl]-1H-indol-5-yl}-5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3- thiazol-4-yl)-N-(2,2,2-trifluoroethyl)prop-2-yn-1-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1002/chem.201901664
  • Primary Citation of Related Structures:  
    6OEY, 6OEX, 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 ...

    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.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trypanothione reductaseB [auth A], A [auth B]495Trypanosoma brucei brucei TREU927Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth B], H [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
M9Y (Subject of Investigation/LOI)
Query on M9Y

Download Ideal Coordinates CCD File 
G [auth B], J [auth A]3-(2-{1-[2-(piperidin-4-yl)ethyl]-1H-indol-5-yl}-5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-4-yl)-N-(2,2,2-trifluoroethyl)prop-2-yn-1-amine
C33 H42 F3 N5 S
RQISOXZUFXHDIM-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D [auth B], I [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B], F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
M9Y Binding MOAD:  6OEX Ki: 1500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.19α = 90
b = 117.19β = 90
c = 224.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2015-04877

Revision History  (Full details and data files)

  • 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