4BGI

Crystal structure of InhA(S94A) mutant in complex with OH-141


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

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

  • 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, E, F
281Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
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 
C, D, E
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
I4I
Query on I4I

Download SDF File 
Download CCD File 
A, B, F
3-hydroxy-N-[(2R,5R,6S,9S,10S,11R)-10-hydroxy-5,11-dimethyl-3,7,12-trioxo-2-(propan-2-yl)-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododecan-6-yl]pyridine-2-carboxamide
C26 H32 N4 O8
ZCNHOXIPSWXQHI-PMWBZGJESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.442α = 90.00
b = 82.450β = 95.63
c = 189.645γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
BUSTERrefinement
XDSdata reduction

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
  • Version 2.0: 2018-11-21
    Type: Atomic model, Data collection, Database references, Source and taxonomy, Structure summary