5YWK

Crystal structure of Arabidopsis thaliana HPPD complexed with Benquitrione-Methyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Guided Discovery of Silicon-Containing Subnanomolar Inhibitor of Hydroxyphenylpyruvate Dioxygenase as a Potential Herbicide.

Qu, R.Y.Nan, J.X.Yan, Y.C.Chen, Q.Ndikuryayo, F.Wei, X.F.Yang, W.C.Lin, H.Y.Yang, G.F.

(2021) J Agric Food Chem 69: 459-473

  • DOI: https://doi.org/10.1021/acs.jafc.0c03844
  • Primary Citation of Related Structures:  
    5YWK, 6M6D

  • PubMed Abstract: 

    4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) has been recognized as one of the most promising targets in the field of herbicide innovation considering the severity of weed resistance currently. In a persistent effort to develop effective HPPD-inhibiting herbicides, a structure-guided strategy was carried out to perform the structural optimization for triketone-quinazoline-2,4-diones, a novel HPPD inhibitor scaffold first discovered in our lab. Herein, starting from the crystal structure of Arabidopsis thaliana ( At )HPPD complexed with 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-( o -tolyl)quinazoline-2,4(1 H ,3 H )-dione ( MBQ ), three subseries of quinazoline-2,4-dione derivatives were designed and prepared by optimizing the hydrophobic interactions between the side chain of the core structure at the R 1 position and the hydrophobic pocket at the active site entrance of At HPPD. 6-(2-Hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-(3-(trimethylsilyl)prop-2-yn-1-yl)quinazoline-2,4(1 H ,3 H )-dione ( 60 ) with the best inhibitory activity against At HPPD was identified to be the first subnanomolar-range At HPPD inhibitor ( K i = 0.86 nM), which significantly outperformed that of the lead compound MBQ ( K i = 8.2 nM). Further determination of the crystal structure of At HPPD in complex with compound 60 (1.85 Å) and the binding energy calculation provided a molecular basis for the understanding of its high efficiency. Additionally, the greenhouse assay indicated that 6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethyl-3-propylquinazoline-2,4(1 H ,3 H )-dione ( 28 ) and compound 60 showed acceptable crop safety against peanut and good herbicidal activity with a broad spectrum. Moreover, compound 28 also showed superior selectivity for wheat at the dosage of 120 g ai/ha and favorable herbicidal efficacy toward the gramineous weeds at the dosage of as low as 30 g ai/ha. We believe that compounds 28 and 60 have promising prospects as new herbicide candidates for wheat and peanut fields.


  • Organizational Affiliation

    Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase
A, B
445Arabidopsis thalianaMutation(s): 0 
Gene Names: HPDPDS1At1g06570F12K11.9
EC: 1.13.11.27
UniProt
Find proteins for P93836 (Arabidopsis thaliana)
Explore P93836 
Go to UniProtKB:  P93836
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP93836
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.753α = 90
b = 95.753β = 90
c = 194.584γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China21672079
National Science Foundation (China)China21332004

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary