How nature bridges the gap: Crystallographic elucidation of pyridomycin binding to InhA

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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This is version 1.3 of the entry. See complete history


Pyridomycin Bridges the Nadh and Substrate Binding Pockets of the Enoyl Reductase Inha

Hartkoorn, R.Pojer, F.Read, J.A.Gingell, H.Neres, J.Horlacher, O.Altmann, K.H.Cole, S.

(2014) Nat Chem Biol 10: 96

  • DOI: https://doi.org/10.1038/nchembio.1405
  • Primary Citation of Related Structures:  
    4BGE, 4BGI, 4BII

  • PubMed Abstract: 

    Pyridomycin, a natural product with potent antituberculosis activity, inhibits a major drug target, the InhA enoyl reductase. Here, we unveil the co-crystal structure and unique ability of pyridomycin to block both the NADH cofactor- and lipid substrate-binding pockets of InhA. This is to our knowledge a first-of-a-kind binding mode that discloses a new means of InhA inhibition. Proof-of-principle studies show how structure-assisted drug design can improve the activity of new pyridomycin derivatives.

  • Organizational Affiliation

    Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland.

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
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.852α = 90
b = 110.285β = 98.21
c = 67.519γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata 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: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other