Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.12 kDa 
• Atom Count: 1668 
• Modelled Residue Count: 193 
• Deposited Residue Count: 216 
• Unique protein chains: 1

6R1P

EthR ligand complex

• DOI: 10.2210/pdb6R1P/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-14 Released: 2020-02-19 
• Deposition Author(s): Pohl, E., Tatum, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds.

Tatum, N.J., Duarte, F., Kamerlin, S.C.L., Pohl, E.

(2019) J Phys Chem Lett 10: 2244-2249

• PubMed: 30965004 
• DOI: 10.1021/acs.jpclett.9b00741
• Primary Citation of Related Structures:  
  6R1P, 6R1S


• PubMed Abstract: 
  

Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.

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Related Citations: 

• New active leads for tuberculosis booster drugs by structure-based drug discovery.
  Tatum, N.J., Liebeschuetz, J.W., Cole, J.C., Frita, R., Herledan, A., Baulard, A.R., Willand, N., Pohl, E.
  (2017) Org Biomol Chem 15: 10245

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Organizational Affiliation: 

Biophysical Sciences Institute , Durham University , Durham DH1 3LE , U.K.

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, Rv3855
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
JPH	A	2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one C17 H17 N5 O3 HUPUXSMUAITIDA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.764	α = 90
b = 121.764	β = 90
c = 33.625	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-03-14 
• Released Date: 2020-02-19 
Deposition Author(s): Pohl, E., Tatum, N.

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release