9JHU | pdb_00009jhu

Complex structure of AtHPPD with inhibitor CLJ788


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.244 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JHU

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Triketone-Indazolones as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibiting-Based Herbicides.

Chen, L.J.Ying, R.N.Wang, X.Q.Xie, D.T.Dong, J.Lin, H.Y.Da-Wei, W.Yang, G.F.

(2025) J Agric Food Chem 73: 1112-1121

  • DOI: https://doi.org/10.1021/acs.jafc.4c08544
  • Primary Citation Related Structures: 
    9JHU

  • PubMed Abstract: 

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a crucial herbicide target in current research, playing an important role in the comprehensive management of resistant weeds. However, the limited crop selectivity and less effectiveness against grass weeds of many existing HPPD inhibitors, limit their further application. To address these issues, a series of novel HPPD inhibitors with fused ring structures were designed and synthesized by introducing an electron-rich indazolone ring and combining it with the classical triketone pharmacophore structure. The cocrystal structure of representative compound III-7 complexed with Arabidopsis thaliana HPPD ( At HPPD) was obtained at 2.0 Å resolution to guide the optimization of the designed inhibitor. The optimization results showed that 5-(2-hydroxy-6-oxocyclohex-1-ene-1-carbonyl)-1,4-dimethyl-2-(3-(methylthio)phenyl)-1,2-dihydro-3 H -indazol-3-one, III-15 , was the most active At HPPD inhibitor, with an IC 50 value of 12 nM, nearly 30 times higher efficacy than mesotrione. Greenhouse herbicidal activity tests demonstrated that compound III-15 exhibited excellent herbicidal potency at 30-120 g ai/ha. Notably, it maintained high safety for peanuts even at 120 g ai/ha. Our results showed that compound III-15 is promising as a new candidate HPPD herbicide for use in the peanut fields.


  • Organizational Affiliation
    • State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.

Macromolecule Content 

  • Total Structure Weight: 44.81 kDa 
  • Atom Count: 2,936 
  • Modeled Residue Count: 381 
  • Deposited Residue Count: 402 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L4A
(Subject of Investigation/LOI)

Query on A1L4A



Download:Ideal Coordinates CCD File
B [auth A]2-(4-methoxyphenyl)-1,4-dimethyl-5-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-indazol-3-one
C23 H22 N2 O5
BLFYOOFXNSCKPF-UHFFFAOYSA-N
CO
(Subject of Investigation/LOI)

Query on CO



Download:Ideal Coordinates CCD File
C [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.244 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.54α = 90
b = 84.447β = 100.96
c = 63.838γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2025-09-17
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Database references