9LIA | pdb_00009lia

Crystal structure of AaHPPD-ZD001 complex

• PDB DOI: https://doi.org/10.2210/pdb9LIA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aedes aegypti
• Expression System: Escherichia coli 0.1288
• Mutation(s): No 


• Deposited: 2025-01-14 Released: 2025-07-02 
• Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Repurposing 4-Hydroxyphenylpyruvate dioxygenase inhibitors as novel agents for mosquito control: A structure-based design approach.

Dong, J., Fu, Y.X., Zheng, B.F., Chen, M.X., Chen, Q., Wishwajith, K., Dong, J., Lin, H.Y., Yang, G.F.

(2025) Int J Biol Macromol 315: 144566-144566

• PubMed: 40412679 
• DOI: https://doi.org/10.1016/j.ijbiomac.2025.144566
• Primary Citation Related Structures: 
  8XTV, 9LIA


• PubMed Abstract: 
  

  Mosquito-borne diseases remain a significant global health burden, necessitating innovative vector control strategies. 4-Hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors, widely used as herbicides, have been recently explored for their potential to disrupt mosquito tyrosine metabolic pathways, offering a novel approach to mosquito control. This study utilized a structure-based rational design strategy to repurpose existing HPPD inhibitors, such as pyrazole-benzene 2,2-dioxothiadiazole and pyrazole-1,3-isoindolinone hybrids, targeting Aedes aegypti HPPD (AaHPPD). Biochemical assays demonstrated that a series of synthesized hybrid compounds exhibited superior inhibitory activity against mosquito-derived HPPD compared to traditional inhibitors, the IC ₅₀ values of compound a9 and compound c14 are 7.70 nM and 53.80 nM, respectively. Crystallographic analysis showed stable inhibitor binding mediated by chelation with metal ions in the active site and π-π interactions with Phe336 and Phe364. C6/36 cell assays further confirmed elevated tyrosine accumulation and significantly affected energy metabolism in the tricarboxylic acid cycle following treatment with the newly designed inhibitors. These findings highlight the potential of repurposed HPPD inhibitors as safe and effective mosquito control agents with novel mechanisms of action.

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Organizational Affiliation: 
• State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
Department of Horticulture and Landscape Gardening, Faculty of Agriculture and Plantation Management, Wayamba University of Sri Lanka, Makandura, Gonawila 60170, Sri Lanka.
Hubei Shizhen Laboratory, Wuhan 430061, PR China; School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China. Electronic address: [e-mail].
State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, PR China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.7 kDa 
• Atom Count: 3,422 
• Modeled Residue Count: 378 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A [auth B]	378	Aedes aegypti	Mutation(s): 0  Gene Names: AAEL014600
UniProt
Find proteins for Q16FX9 (Aedes aegypti) Explore Q16FX9  Go to UniProtKB:  Q16FX9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L7D	C [auth B]	5-(1-methyl-5-oxidanyl-pyrazol-4-yl)carbonyl-2-(phenylmethyl)isoindole-1,3-dione C20 H15 N3 O4 GNZCKXMCPWJIFN-UHFFFAOYSA-N
CO	B	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.984	α = 90
b = 83.841	β = 101.91
c = 59.184	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release