4BII

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

• PDB DOI: https://doi.org/10.2210/pdb4BII/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-10 Released: 2013-12-04 
• Deposition Author(s): Read, J.A., Gingell, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

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

• 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)

Macromolecule Content

• Total Structure Weight: 117.83 kDa 
• Atom Count: 8,164 
• Modelled Residue Count: 1,027 
• Deposited Residue Count: 1,076 
• 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	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PYW	F [auth A], H [auth B], J [auth D]	Pyridomycin C27 H32 N4 O8 WHIKSLGSXKIHCA-IGCCMALHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PYW	BindingDB:  4BII	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: 1.95 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.852	α = 90
b = 110.285	β = 98.21
c = 67.519	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Read, J.A., Gingell, H.

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: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other