9VQ5 | pdb_00009vq5

Crystal structure of Peroxiredoxin I in complex with SAC

• PDB DOI: https://doi.org/10.2210/pdb9VQ5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-07-04 Released: 2026-07-08 
• Deposition Author(s): Zhu, Y.Y., Xu, H., Zhang, H., Luo, C.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Design and evaluation of peroxiredoxin 1 agonist based on scaffold hopping of salvianolic acids and combinatorial click chemistry.

Zhu, Y.Y., Chen, S., Zhang, S.N., Zhu, Y.S., Liang, J.Y., Wang, Z.Y., Wang, X.M., Liu, J.J., Liu, P.F., Li, Z.H., Xiao, W.L., Xu, H., Luo, C., Xiong, H., Zhang, H.

(2026) Acta Pharmacol Sin 47: 1965-1979

• PubMed: 41803461 
• DOI: https://doi.org/10.1038/s41401-026-01765-1
• Primary Citation Related Structures: 
  9VQ5


• PubMed Abstract: 
  

  Peroxiredoxin 1 (PRDX1) is a pivotal antioxidant enzyme maintaining intracellular reactive oxygen species (ROS) balance. Deficiency of PRDX1 aggravates oxidative stress-related pathologies, whereas enhanced PRDX1 activity confers cytoprotection. Small-molecule agonists boosting PRDX1 peroxidase activity hold therapeutic promise, yet to date only two such agonists-rosmarinic acid (RA) and salvianolic acid B (SAB)-have been reported, both by our laboratory. These polyphenolic compounds are chemically rigid and recalcitrant to modification. Here, we resolved the crystal structure of PRDX1 in complex with salvianolic acid C (SAC), revealing a conserved danshensu substructure shared by SAC, RA, and SAB. Guided by this pharmacophore, we designed a scaffold hopping core structure and generated 160 derivatives via in situ click reaction. Among them, LC-PDA-01, a non-polyphenolic scaffold, exhibited the highest PRDX1 activation (EC ₅₀  = 111.8 nM). This work discloses the first structurally tractable PRDX1 agonist and highlights combinatorial click chemistry's utility in transforming natural product motifs into drug-like molecules.

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Organizational Affiliation: 
• School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education and Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming, 650050, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, 100049, China. [e-mail].
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China. [e-mail].
Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China. [e-mail].
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China. [e-mail].
Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China. [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: 39.17 kDa 
• Atom Count: 3,117 
• Modeled Residue Count: 331 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-1	A, B	175	Homo sapiens	Mutation(s): 2  Gene Names: PRDX1, PAGA, PAGB, TDPX2 EC: 1.11.1.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q06830 (Homo sapiens) Explore Q06830  Go to UniProtKB:  Q06830
PHAROS:  Q06830 GTEx:  ENSG00000117450

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ES6	C [auth A]	(2~{R})-3-[3,4-bis(oxidanyl)phenyl]-2-[(~{E})-3-[2-[3,4-bis(oxidanyl)phenyl]-7-oxidanyl-1-benzofuran-4-yl]prop-2-enoyl]oxy-propanoic acid C26 H20 O10 GCJWPRRNLSHTRY-VURDRKPISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.697	α = 90
b = 78.709	β = 90
c = 81.346	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-08 
Deposition Author(s): Zhu, Y.Y., Xu, H., Zhang, H., Luo, C.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB0830300

Revision History  

• Version 1.0: 2026-07-08
  Type: Initial release
  
• Version 1.1: 2026-08-26
  Changes: Database references