5J3L | pdb_00005j3l

Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with 1-((2-cyclopentylethyl)sulfonyl)pyrrolidine at 1.66A resolution

• PDB DOI: https://doi.org/10.2210/pdb5J3L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-31 Released: 2017-03-29 
• Deposition Author(s): Blaszczyk, M., Surade, S., Nikiforov, P.O., Abell, C., Blundell, T.L.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Bill & Melinda Gates Foundation, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Fragment-Sized EthR Inhibitors Exhibit Exceptionally Strong Ethionamide Boosting Effect in Whole-Cell Mycobacterium tuberculosis Assays.

Nikiforov, P.O., Blaszczyk, M., Surade, S., Boshoff, H.I., Sajid, A., Delorme, V., Deboosere, N., Brodin, P., Baulard, A.R., Barry, C.E., Blundell, T.L., Abell, C.

(2017) ACS Chem Biol 12: 1390-1396

• PubMed: 28314097 
• DOI: https://doi.org/10.1021/acschembio.7b00091
• Primary Citation Related Structures: 
  5IOY, 5IOZ, 5IP6, 5IPA, 5J1R, 5J1U, 5J1Y, 5J3L


• PubMed Abstract: 
  

  Small-molecule inhibitors of the mycobacterial transcriptional repressor EthR have previously been shown to act as boosters of the second-line antituberculosis drug ethionamide. Fragment-based drug discovery approaches have been used in the past to make highly potent EthR inhibitors with ethionamide boosting activity both in vitro and ex vivo. Herein, we report the development of fragment-sized EthR ligands with nanomolar minimum effective concentration values for boosting the ethionamide activity in Mycobacterium tuberculosis whole-cell assays.

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Organizational Affiliation: 
• Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.
Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States.
CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, Université de Lille , F-59000 Lille, France.
Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town 7935, South Africa.

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)

Macromolecule Content 

• Total Structure Weight: 24.01 kDa 
• Atom Count: 1,549 
• Modeled Residue Count: 193 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A	216	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ethR, etaR, MT3970
UniProt
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMC1  Go to UniProtKB:  P9WMC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6FR	B [auth A]	1-[(2-cyclopentylethyl)sulfonyl]pyrrolidine C11 H21 N O2 S UAJGQMZYCCWBAX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6FR	BindingDB:  5J3L	Kd: 1.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.13	α = 90
b = 121.13	β = 90
c = 34.05	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Blaszczyk, M., Surade, S., Nikiforov, P.O., Abell, C., Blundell, T.L.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--
Bill & Melinda Gates Foundation	United States	--
European Union		--

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-05-31
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description