3Q0V | pdb_00003q0v

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 52.57 kDa
Atom Count: 3,221
Modeled Residue Count: 382
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WMC1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LL4 Query on LL4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.228 (Depositor), 0.227 (DCC)
R-Value Work: 0.166 (Depositor), 0.166 (DCC)
R-Value Observed: 0.169 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-01-11

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.