8P8K | pdb_00008p8k

Acyl-ACP thioesterase from Lemna paucicostata in complex with a thiazolopyridine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.223 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

A Study in Scaffold Hopping: Discovery and Optimization of Thiazolopyridines as Potent Herbicides That Inhibit Acyl-ACP Thioesterase.

Abel, S.A.G.Alnafta, N.Asmus, E.Bollenbach-Wahl, B.Braun, R.Dittgen, J.Endler, A.Frackenpohl, J.Freigang, J.Gatzweiler, E.Heinemann, I.Helmke, H.Laber, B.Lange, G.Machettira, A.McArthur, G.Muller, T.Odaybat, M.Reingruber, A.M.Roth, S.Rosinger, C.H.Schmutzler, D.Schulte, W.Stoppel, R.Tiebes, J.Volpin, G.Barber, D.M.

(2023) J Agric Food Chem 71: 18212-18226

  • DOI: https://doi.org/10.1021/acs.jafc.3c02490
  • Primary Citation Related Structures: 
    8P8K

  • PubMed Abstract: 

    In the search for new chemical entities that can control resistant weeds by addressing novel modes of action (MoAs), we were interested in further exploring a compound class that contained a 1,8-naphthyridine core. By leveraging scaffold hopping methodologies, we were able to discover the new thiazolopyridine compound class that act as potent herbicidal molecules. Further biochemical investigations allowed us to identify that the thiazolopyridines inhibit acyl-acyl carrier protein (ACP) thioesterase (FAT), with this being further confirmed via an X-ray cocrystal structure. Greenhouse trials revealed that the thiazolopyridines display excellent control of grass weed species in pre-emergence application coupled with dose response windows that enable partial selectivity in certain crops.


  • Organizational Affiliation
    • Research and Development, Weed Control Research, Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany.

Macromolecule Content 

  • Total Structure Weight: 74.02 kDa 
  • Atom Count: 4,528 
  • Modeled Residue Count: 552 
  • Deposited Residue Count: 640 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl-ACP thioesteraseA [auth AAA],
B [auth BBB]
320Lemna aequinoctialisMutation(s): 0 
EC: 3.1.2

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.168α = 90
b = 93.168β = 90
c = 135.957γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-09-20 
  • Deposition Author(s): Freigang, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references