InhA in complex with a DNA encoded library hit

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
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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 U S A 113: E7780

  • DOI: https://doi.org/10.1073/pnas.1610978113
  • Primary Citation of Related Structures:  
    5G0S, 5G0T, 5G0U, 5G0V, 5G0W

  • 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 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 (10 11 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
269Mycobacterium tuberculosis H37RvMutation(s): 0 
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
JDD BindingDB:  5G0V Kd: min: 37, max: 1.00e+5 (nM) from 2 assay(s)
IC50: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.151α = 90
b = 111.727β = 98.3
c = 67.813γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description