4NEV | pdb_00004nev

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor EP127 (5-{5-[1-(PYRROLIDIN-1-YL)CYCLOHEXYL]-1,3-THIAZOL-2-YL}-1H-INDOLE)

PDB DOI: https://doi.org/10.2210/pdb4NEV/pdb

Classification: Oxidoreductase/Oxidoreductase inhibitor
Organism(s): Trypanosoma brucei brucei TREU927
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-30 Released: 2014-05-14
Deposition Author(s): Persch, E., Bryson, S., Pai, E.F., Krauth-Siegel, R.L., Diederich, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.258 (Depositor), 0.259 (DCC)
R-Value Work:
0.234 (Depositor), 0.231 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase.

Persch, E., Bryson, S., Todoroff, N.K., Eberle, C., Thelemann, J., Dirdjaja, N., Kaiser, M., Weber, M., Derbani, H., Brun, R., Schneider, G., Pai, E.F., Krauth-Siegel, R.L., Diederich, F.

(2014) ChemMedChem 9: 1880-1891

PubMed: 24788386 Search on PubMed
DOI: https://doi.org/10.1002/cmdc.201402032
Primary Citation Related Structures:
4NEV, 4NEW

PubMed Abstract:
The causative agents of the parasitic disease human African trypanosomiasis belong to the family of trypanosomatids. These parasitic protozoa exhibit a unique thiol redox metabolism that is based on the flavoenzyme trypanothione reductase (TR). TR was identified as a potential drug target and features a large active site that allows a multitude of possible ligand orientations, which renders rational structure-based inhibitor design highly challenging. Herein we describe the synthesis, binding properties, and kinetic analysis of a new series of small-molecule inhibitors of TR. The conjunction of biological activities, mutation studies, and virtual ligand docking simulations led to the prediction of a binding mode that was confirmed by crystal structure analysis. The crystal structures revealed that the ligands bind to the hydrophobic wall of the so-called "mepacrine binding site". The binding conformation and potency of the inhibitors varied for TR from Trypanosoma brucei and T. cruzi.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 110.63 kDa
Atom Count: 7,667
Modeled Residue Count: 970
Deposited Residue Count: 990
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypanothione reductase	A, B	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q389T8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
2JR Query on 2JR Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B], P [auth B]	5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole C₂₁ H₂₅ N₃ S MXBHIYKTGVOQMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain P [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.258 (Depositor), 0.259 (DCC)
R-Value Work: 0.234 (Depositor), 0.231 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.2	α = 90
b = 117.2	β = 90
c = 224.6	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-14
Type: Initial release
Version 1.1: 2014-08-13
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary