4BGE

Crystal structure of InhA(S94A) mutant in complex with pyridomycin

• PDB DOI: https://doi.org/10.2210/pdb4BGE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-03-26 Released: 2013-12-04 
• Deposition Author(s): Pojer, F., Hartkoorn, R.C., Cole, S.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.278 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA.

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

(2014) Nat Chem Biol 10: 96-98

• PubMed: 24292073 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 174.48 kDa 
• Atom Count: 12,612 
• Modelled Residue Count: 1,558 
• Deposited Residue Count: 1,614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D, E, F	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: inhA, Rv1484, MTCY277.05 EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1  Go to UniProtKB:  P9WGR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYW	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	Pyridomycin C27 H32 N4 O8 WHIKSLGSXKIHCA-IGCCMALHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PYW	BindingDB:  4BGE	Ki: min: 4550, max: 6500 (nM) from 3 assay(s)
		IC50: min: 3430, max: 6000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.278 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.601	α = 90
b = 83.049	β = 94.84
c = 190.682	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Pojer, F., Hartkoorn, R.C., Cole, S.T.

Revision History  

• 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: 2018-11-21
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-10-16
  Changes: Data collection, Other
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description