8J3C | pdb_00008j3c

Crystal structure of AtHPPD-Y19623 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.205 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Triketone-Quinazolinone Hybrids as Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors.

Zhang, W.J.Dong, Y.J.Zhou, S.M.Ying, R.N.Cai, Z.M.Zhao, J.Wang, D.W.Lin, H.Y.

(2026) J Agric Food Chem 74: 24185-24197

  • DOI: https://doi.org/10.1021/acs.jafc.6c05378
  • Primary Citation Related Structures: 
    8J3C, 9WGC

  • PubMed Abstract: 

    4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is a promising target for new herbicide research. To develop new HPPD-inhibiting herbicides, we used a scaffold-hopping strategy by introducing a quinazolinone ring and combining it with the classic triketone pharmacophore, designing and synthesizing a series of novel HPPD inhibitors with a fused-ring architecture. The results showed that II-series of compounds exhibited excellent inhibitory activity against Arabidopsis thaliana (At) HPPD, with IC50 values 0.5- to 2.5-fold lower than those of mesotrione. Moreover, we obtained the crystal structure of AtHPPD-II-36 complex at a resolution of 1.8 Å. Importantly, II-36 exhibited high safety to wheat and outstanding herbicidal efficacy against Echinochloa crus-galli, Digitaria sanguinalis, and Bromus japonicus at a dosage of 30 g ai/ha. Our study provides a valuable example for designing novel HPPD inhibitors with enhanced herbicidal activity and improved crop selectivity.


  • Organizational Affiliation
    • State Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan430079, P.R. China.

Macromolecule Content 

  • Total Structure Weight: 46.39 kDa 
  • Atom Count: 3,150 
  • Modeled Residue Count: 379 
  • Deposited Residue Count: 417 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase417Arabidopsis 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
SZO

Query on SZO



Download:Ideal Coordinates CCD File
C [auth A]5-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-phenyl-quinazolin-4-one
C22 H18 N2 O4
YZIDJGZJJXADLD-UHFFFAOYSA-N
CO

Query on CO



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.205 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.107α = 90
b = 83.988β = 100.51
c = 62.283γ = 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: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2026-08-26
    Changes: Database references