9KOZ | pdb_00009koz

Crystal structure of Arabidopsis thaliana HPPD complexed with iptriazopyrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.266 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.218 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mechanism of Herbicidal Action and Rice Selectivity of Iptriazopyrid: A Novel Azole Carboxamide-Based Inhibitor of 4-Hydroxyphenylpyruvate Dioxygenase.

Nishio, T.Nishijima, N.Kubota, T.Furuhata, Y.Nanao, Y.Permana, H.Furuhashi, T.Kato, Y.

(2025) J Agric Food Chem 73: 15950-15958

  • DOI: https://doi.org/10.1021/acs.jafc.4c11831
  • Primary Citation of Related Structures:  
    9KOY, 9KOZ, 9KP0

  • PubMed Abstract: 

    4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors are widely used as herbicides. However, the emergence of herbicide-resistant weeds necessitates the development of new herbicides with more diverse chemical structures. Therefore, we evaluated the herbicidal and HPPD inhibitory activities of iptriazopyrid, a novel azole carboxamide compound. Phytotoxic tests on Echinochloa crus-galli demonstrated that iptriazopyrid caused chlorosis at a concentration approximately 10 times lower than that required for the common commercial HPPD inhibitor mesotrione. Furthermore, iptriazopyrid showed strong selectivity for Oryza sativa over the weed in the greenhouse-scale experiment. X-ray crystallography and in vitro inhibitory assays revealed that iptriazopyrid was bound to the enzyme active pocket of HPPD and worked as a slow-binding inhibitor. These findings indicate that this inhibitor has potent herbicidal activity with a chemical structure different from those of existing HPPD inhibitors. Thus, it has potential applications as a novel scaffold in herbicide development.


  • Organizational Affiliation
    • Molecular Biosystems Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase
A, B, C, D
444Arabidopsis 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L59 (Subject of Investigation/LOI)
Query on A1L59

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
iptriazopyrid
C15 H15 F3 N6 O4 S
ODXFUPRPCAYZLK-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.266 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.218 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.16α = 90
b = 96.04β = 92.806
c = 97.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references