4QXM

Crystal structure of the InhA:GSK_SB713 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.196 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

N-Benzyl-4-((heteroaryl)methyl)benzamides: A New Class of Direct NADH-Dependent 2-trans Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors with Antitubercular Activity.

Guardia, A.Gulten, G.Fernandez, R.Gomez, J.Wang, F.Convery, M.Blanco, D.Martinez, M.Perez-Herran, E.Alonso, M.Ortega, F.Rullas, J.Calvo, D.Mata, L.Young, R.Sacchettini, J.C.Mendoza-Losana, A.Remuinan, M.Ballell Pages, L.Castro-Pichel, J.

(2016) Chemmedchem 11: 687-701

  • DOI: 10.1002/cmdc.201600020

  • PubMed Abstract: 
  • Isoniazid (INH) remains one of the cornerstones of antitubercular chemotherapy for drug-sensitive strains of M. tuberculosis bacteria. However, the increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains contai ...

    Isoniazid (INH) remains one of the cornerstones of antitubercular chemotherapy for drug-sensitive strains of M. tuberculosis bacteria. However, the increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains containing mutations in the KatG enzyme, which is responsible for the activation of INH into its antitubercular form, have rendered this drug of little or no use in many cases of drug-resistant tuberculosis. Presented herein is a novel family of antitubercular direct NADH-dependent 2-trans enoyl-acyl carrier protein reductase (InhA) inhibitors based on an N-benzyl-4-((heteroaryl)methyl)benzamide template; unlike INH, these do not require prior activation by KatG. Given their direct InhA target engagement, these compounds should be able to circumvent KatG-related resistance in the clinic. The lead molecules were shown to be potent inhibitors of InhA and showed activity against M. tuberculosis bacteria. This new family of inhibitors was found to be chemically tractable, as exemplified by the facile synthesis of analogues and the establishment of structure-activity relationships. Furthermore, a co-crystal structure of the initial hit with the enzyme is disclosed, providing valuable information toward the design of new InhA inhibitors for the treatment of MDR/XDR tuberculosis.


    Organizational Affiliation

    Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain. ana.a.guardia@gsk.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, C, E, G
269Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: inhA
EC: 1.3.1.9
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGR1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, C, E, G
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
713
Query on 713

Download SDF File 
Download CCD File 
A, C
N-(2-chloro-4-fluorobenzyl)-4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]benzamide
C20 H19 Cl F N3 O
PUPDWYSTSLHVKJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.196 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.359α = 90.00
b = 83.627β = 115.31
c = 86.037γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2016-04-27
    Type: Database references