8RX6 | pdb_00008rx6

Mycothione reductase from Mycobacterium tuberculosis in complex with Respiri-1093

PDB DOI: https://doi.org/10.2210/pdb8RX6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-02-06 Released: 2025-08-20
Deposition Author(s): Oorts, L., Osipov, E.M., Beelen, S., Strelkov, S.V.
Funding Organization(s): Research Foundation - Flanders (FWO), European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.42 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.233 (Depositor), 0.234 (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 1.1 of the entry. See complete history.

Literature

Crystal structure of Mycobacterium tuberculosis mycothione reductase in complex with a specific inhibitor reveals competition with NADP(H) binding.

Oorts, L., Osipov, E.M., Beelen, S., Smiejkowska, N., Van Calster, K., Lamprecht, D., Temmerman, K., Van Aerschot, A., Cappoen, D., Cos, P., Strelkov, S.V.

(2026) FEBS Lett 600: 2143-2153

PubMed: 42175780 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.70336
Primary Citation Related Structures:
8RX4, 8RX5, 8RX6

PubMed Abstract:
Tuberculosis (TB) remains a major health threat, while the increasing occurrence of drug-resistant strains underscores the need for new antitubercular drugs. A promising strategy to combat TB is based on disrupting the mycobacterial redox homeostasis by inhibiting an NADPH-dependent oxidoreductase, mycothione reductase (Mtr). Using high-throughput screening, we recently identified potent and selective Mtr inhibitors. Here we report high-resolution X-ray structures of Mtr from Mycobacterium tuberculosis and Mycobacterium xenopi, including the M. tuberculosis enzyme complexed with a novel inhibitor, Respiri-1093. Our findings demonstrate that Respiri-1093 competes with the NADP(H) binding rather than mycothione binding. Analysis of the binding site explains the observed selectivity of the inhibitor towards the M. tuberculosis enzyme. These results provide a structural basis for rational drug design.

Organizational Affiliation

Laboratory of Microbiology, Parasitology and Hygiene, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium.

Macromolecule Content

Total Structure Weight: 305.48 kDa
Atom Count: 21,429
Modeled Residue Count: 2,754
Deposited Residue Count: 2,754
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycothione reductase	A, B, C, D, E A, B, C, D, E, F	459	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: mtr, gorA, Rv2855 EC: 1.8.1.15
UniProt
Find proteins for P9WHH3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHH3 Go to UniProtKB: P9WHH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WHH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] L [auth E] G [auth A], H [auth B], I [auth C], J [auth D], L [auth E], N [auth F]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain L [auth E] Focus chain N [auth F]
A1H3R (Subject of Investigation/LOI) Query on A1H3R Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain K [auth D] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D]	K [auth D], M [auth E]	(3~{S})-4-[4-(1-benzothiophen-3-yl)-6,7,8,9-tetrahydro-5~{H}-pyrimido[4,5-d]azepin-2-yl]-3-methyl-morpholine C₂₁ H₂₄ N₄ O S JTACVXYKEBRWKG-AWEZNQCLSA-N		Interactions Focus chain K [auth D] Focus chain M [auth E] Interactions & Density Focus chain K [auth D] Focus chain M [auth E]