4BII

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/nchembio.1405
  • Primary Citation of Related Structures:  

  • 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 substr ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download SDF File 
Download CCD File 
A, B, D
Pyridomycin
C27 H32 N4 O8
WHIKSLGSXKIHCA-IGCCMALHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PYWIC50: 6000 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.852α = 90.00
b = 110.285β = 98.21
c = 67.519γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
BUSTERrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references