9JS2 | pdb_00009js2

Complex structure of AtHPPD with inhibitor YH23570


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Design, Synthesis, and Bioactivity of Triketone-quinoxalin-2-ones as a Novel HPPD Inhibition Herbicide.

Cai, Z.M.Ying, R.N.Wang, X.Q.Bai, R.Y.Sun, A.Kandegama, W.Lin, H.Y.Wang, D.W.Yang, G.F.

(2025) J Agric Food Chem 73: 27328-27337

  • DOI: https://doi.org/10.1021/acs.jafc.5c08188
  • Primary Citation Related Structures: 
    9JS2

  • PubMed Abstract: 

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) is recognized as one of the most promising herbicide targets for sustainable weed control in modern agricultural practices. To address agricultural demands, we designed and synthesized a novel series of triketone-quinoxalin-2-ones as potent HPPD inhibitors. In vitro evaluation revealed that the newly synthesized compounds demonstrated remarkable Arabidopsis thaliana HPPD ( At HPPD) inhibitory activity. Significantly, compound 23 , 3-(4-chloro-2-fluorophenyl)-6-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,5-dimethylquinoxalin-2(1 H )-one, showed the strongest At HPPD inhibition with an IC 50 value of 0.034 μM, 10-fold more potent than mesotrione (IC 50 = 0.350 μM). Furthermore, the postemergence herbicidal activity evaluation showed that compound 35 exhibited 100% inhibition of Digitaria sanguinalis , Amaranthus retroflexus , Chenopodium serotinum , and Abutilon theophrasti at 150 g ai/ha, and 90% inhibition of Setaria viridis , showing enhanced activity compared to mesotrione. The crystal structure of the At HPPD -35 complex demonstrated that compound 35 engaged in a key bidentate chelating interaction with the metal ion in the catalytic active site and a π-π interaction with Phe381 and Phe424. Moreover, 35 established hydrophobic interactions with Leu427, Leu368, and Met335. These results indicate that the triketone-quinoxalin-2-one hybrid is a promising scaffold and 35 can be considered a viable lead compound for the development of HPPD inhibitors.


  • Organizational Affiliation
    • State Key Laboratory of Green Pesticide, 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 dioxygenase402Arabidopsis 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
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.153α = 90
b = 83.737β = 100.11
c = 65.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references