4P8C | pdb_00004p8c

Crystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor QN127

• PDB DOI: https://doi.org/10.2210/pdb4P8C/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-12-10 
• Deposition Author(s): Neres, J., Pojer, F., Cole, S.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1.

Neres, J., Hartkoorn, R.C., Chiarelli, L.R., Gadupudi, R., Pasca, M.R., Mori, G., Venturelli, A., Savina, S., Makarov, V., Kolly, G.S., Molteni, E., Binda, C., Dhar, N., Ferrari, S., Brodin, P., Delorme, V., Landry, V., de Jesus Lopes Ribeiro, A.L., Farina, D., Saxena, P., Pojer, F., Carta, A., Luciani, R., Porta, A., Zanoni, G., De Rossi, E., Costi, M.P., Riccardi, G., Cole, S.T.

(2015) ACS Chem Biol 10: 705-714

• PubMed: 25427196 
• DOI: https://doi.org/10.1021/cb5007163
• Primary Citation Related Structures: 
  4CVY, 4P8C, 4P8K, 4P8L, 4P8M, 4P8N, 4P8P, 4P8T, 4P8Y


• PubMed Abstract: 
  

  Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 μM, Ty38c is bactericidal and active against intracellular bacteria. To investigate its mechanism of action, we isolated mutants resistant to Ty38c and sequenced their genomes. Mutations were found in rv3405c, coding for the transcriptional repressor of the divergently expressed rv3406 gene. Biochemical studies clearly showed that Rv3406 decarboxylates Ty38c into its inactive keto metabolite. The actual target was then identified by isolating Ty38c-resistant mutants of an M. tuberculosis strain lacking rv3406. Here, mutations were found in dprE1, encoding the decaprenylphosphoryl-d-ribose oxidase DprE1, essential for biogenesis of the mycobacterial cell wall. Genetics, biochemical validation, and X-ray crystallography revealed Ty38c to be a noncovalent, noncompetitive DprE1 inhibitor. Structure-activity relationship studies generated a family of DprE1 inhibitors with a range of IC50's and bactericidal activity. Co-crystal structures of DprE1 in complex with eight different quinoxaline analogs provided a high-resolution interaction map of the active site of this extremely vulnerable target in M. tuberculosis.

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Organizational Affiliation: 
• †More Medicines for Tuberculosis (MM4TB) Consortium (www.mm4tb.org).
‡Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.
§Department of Biology and Biotecnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy.
∥Tydock Pharma, srl Via Campi 183, 41125 Modena, Italy.
⊥Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 183, 41126 Modena, Italy.
#A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia.
∇Inserm U1019 - CNRS UMR 8204, Institut Pasteur de Lille, Université de Lille, 1 rue du Professeur Calmette, 59019, Lille, France.
○Department of Chemistry and Pharmacy, University of Sassari, 07100 Sassari, Italy.
◆Department of Chemistry, University of Pavia, 27100 Pavia, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.18 kDa 
• Atom Count: 7,087 
• Modeled Residue Count: 865 
• Deposited Residue Count: 960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable decaprenylphosphoryl-beta-D-ribose oxidase	A, B	480	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dprE1, Rv3790, MT3898 EC: 1 (PDB Primary Data), 1.1.98.3 (UniProt)
UniProt
Find proteins for P9WJF1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJF1  Go to UniProtKB:  P9WJF1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
Y22	D [auth A], H [auth B]	6-(trifluoromethyl)-3-{[4-(trifluoromethyl)benzyl]amino}quinoxaline-2-carboxylic acid C18 H11 F6 N3 O2 FEJSMMIZTOMLEL-UHFFFAOYSA-N
2J3	F [auth A]	(2R)-2-{[(2R)-2-{[(2R)-2-hydroxypropyl]oxy}propyl]oxy}propan-1-ol C9 H20 O4 LCZVSXRMYJUNFX-IWSPIJDZSA-N
IMD	E [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
Y22	BindingDB:  4P8C	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.678	α = 90
b = 84.158	β = 103.17
c = 80.905	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Neres, J., Pojer, F., Cole, S.T.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2015-04-01
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description