9KOY | pdb_00009koy

Crystal structure of Oryza sativa HPPD complexed with iptriazopyrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.285 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.211 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 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 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.

Macromolecule Content 

  • Total Structure Weight: 95.21 kDa 
  • Atom Count: 5,948 
  • Modeled Residue Count: 777 
  • Deposited Residue Count: 892 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
4-hydroxyphenylpyruvate dioxygenase
A, B
446Oryza sativaMutation(s): 0 
UniProt
Find proteins for Q6H4V1 (Oryza sativa subsp. japonica)
Explore Q6H4V1 
Go to UniProtKB:  Q6H4V1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6H4V1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L59
(Subject of Investigation/LOI)

Query on A1L59



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
iptriazopyrid
C15 H15 F3 N6 O4 S
ODXFUPRPCAYZLK-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CO

Query on CO



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.285 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.211 (DCC) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.61α = 90
b = 158.61β = 90
c = 84.075γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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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