5G0W

InhA in complex with a DNA encoded library hit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Cofactor-Specific, Bactericidal Mycobacterium Tuberculosis Inha Inhibitors Using DNA-Encoded Library Technology

Soutter, H.H.Centrella, P.Clark, M.A.Cuozzo, J.W.Dumelin, C.E.Guie, M.-A.Habeshian, S.Keefe, A.D.Kennedy, K.M.Sigel, E.A.Troast, D.M.Zhang, Y.Ferguson, A.D.Davies, G.Stead, E.R.Breed, J.Madhavapeddi, P.Read, J.A.

(2016) Proc.Natl.Acad.Sci.USA 113: E7780

  • DOI: 10.1073/pnas.1610978113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current front ...

    Millions of individuals are infected with and die from tuberculosis (TB) each year, and multidrug-resistant (MDR) strains of TB are increasingly prevalent. As such, there is an urgent need to identify novel drugs to treat TB infections. Current frontline therapies include the drug isoniazid, which inhibits the essential NADH-dependent enoyl-acyl-carrier protein (ACP) reductase, InhA. To inhibit InhA, isoniazid must be activated by the catalase-peroxidase KatG. Isoniazid resistance is linked primarily to mutations in the katG gene. Discovery of InhA inhibitors that do not require KatG activation is crucial to combat MDR TB. Multiple discovery efforts have been made against InhA in recent years. Until recently, despite achieving high potency against the enzyme, these efforts have been thwarted by lack of cellular activity. We describe here the use of DNA-encoded X-Chem (DEX) screening, combined with selection of appropriate physical properties, to identify multiple classes of InhA inhibitors with cell-based activity. The utilization of DEX screening allowed the interrogation of very large compound libraries (1011 unique small molecules) against multiple forms of the InhA enzyme in a multiplexed format. Comparison of the enriched library members across various screening conditions allowed the identification of cofactor-specific inhibitors of InhA that do not require activation by KatG, many of which had bactericidal activity in cell-based assays.


    Organizational Affiliation

    Therapeutic Discovery Sciences, X-Chem Pharmaceuticals, Waltham, MA 02453; hsoutter@x-chemrx.com Jon.Read@astrazeneca.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOYL-ACYL CARRIER PROTEIN REDUCTASE
A, B, C, D
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9NU
Query on 9NU

Download SDF File 
Download CCD File 
B, C
(2S,4S)-N-methyl-4-[[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-2-[[4-(pyrazol-1-ylmethyl)phenyl]carbonylamino]butanoyl]amino]-1-(phenylcarbonyl)pyrrolidine-2-carboxamide
C32 H40 N6 O5
CTUBNTAXILQBGR-FBZFJNBBSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.428α = 90.00
b = 112.729β = 97.66
c = 67.970γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
Aimlessdata scaling
MOSFLMdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-03-22 
  • Released Date: 2016-11-30 
  • Deposition Author(s): Read, J.A., Breed, J.

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references