3Q0V

ETHR From mycobacterium tuberculosis in complex with compound bdm31369

• PDB DOI: https://doi.org/10.2210/pdb3Q0V/pdb

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


• Deposited: 2010-12-16 Released: 2012-01-11 
• Deposition Author(s): Flipo, M., Desroses, M., Dirie, B., Carette, X., Leroux, F., Lens, Z., Rucktooa, P., Leroux, F., Piveteau, C., Demirkaya, F., Locht, C., Villeret, V., Christophe, T., Jeon, H.K., Brodin, P., Deprez, B., Baulard, A., Willand, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Literature

Design, synthesis and optimization of new EthR inhibitors. A new alternative approach to fight tuberculosis by boosting ethionamide

Flipo, M., Desroses, M., Dirie, B., Carette, X., Leroux, F., Lens, Z., Rucktooa, P., Leroux, F., Piveteau, C., Demirkaya, F., Locht, C., Villeret, V., Christophe, T., Jeon, H.K., Brodin, P., Deprez, B., Baulard, A., Willand, N.

To be published.

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: 52.57 kDa 
• Atom Count: 3,221 
• Modelled Residue Count: 382 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional regulator EthR	A, B	236	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ethR, etaR, MT3970, Rv3855
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
LL4	C [auth A], D [auth B]	4-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one C17 H23 N3 O2 S QWPAQBJBWLSPSH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
LL4	BindingDB:  3Q0V	IC50: 900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.228 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.56	α = 90
b = 121.56	β = 90
c = 33.77	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Flipo, M., Desroses, M., Dirie, B., Carette, X., Leroux, F., Lens, Z., Rucktooa, P., Leroux, F., Piveteau, C., Demirkaya, F., Locht, C., Villeret, V., Christophe, T., Jeon, H.K., Brodin, P., Deprez, B., Baulard, A., Willand, N.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations