9M82 | pdb_00009m82

Crystal Structure of Human IDH1 in Complex with Kinsenoside

• PDB DOI: https://doi.org/10.2210/pdb9M82/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-11 Released: 2026-03-18 
• Deposition Author(s): Ouyang, S., Zhao, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 
  0.301 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Kinsenoside Targets IDH1 to Restore Microglial Immune-Metabolic Homeostasis for Alzheimer's Disease Therapy.

Li, Q., Liao, Y., Zhao, Y.B., Wu, H., Jin, T., Li, S., Liu, Y., Li, P., Ouyang, S., Li, Z., Xia, Y., Hua, Q., Pan, R.Y., Yuan, Z.

(2026) Adv Sci (Weinh) 13: e75125-e75125

• PubMed: 41980178 
• DOI: https://doi.org/10.1002/advs.75125
• Primary Citation Related Structures: 
  9M82


• PubMed Abstract: 
  

  Dysregulated tricarboxylic acid (TCA) cycle activity is increasingly recognized as a contributor to Alzheimer's disease (AD) pathogenesis, yet the mechanistic underpinnings of the relationship remain unclear. Here, we identify isocitrate dehydrogenase 1 (IDH1), a key enzyme in the TCA cycle, as a critical pathogenic driver of AD in microglia. IDH1 expression was markedly upregulated in microglia from both AD patients and 5×FAD mice. Elevated IDH1 promoted excessive cytosolic citrate consumption, which restricted citrate shuttling into mitochondria and impaired mitochondrial TCA cycle function. This citrate metabolic imbalance further disrupted epigenetic regulation, thereby exacerbating AD-related pathological processes. Using structure-based screening and co-crystallization analysis, we identified Kinsenoside (KIN), a natural small molecule, as a selective competitive inhibitor of IDH1 that binds to its isocitrate-binding pocket. Targeting IDH1 with KIN inhibited its activity, which restored intracellular citrate distribution, reactivated mitochondrial TCA cycle flux, and reestablished metabolic homeostasis. Notably, this intervention not only attenuated neuroinflammation but also reduced β-amyloid (Aβ) deposition and significantly improved cognitive performance in 5×FAD mice. Collectively, our findings establish IDH1-mediated metabolic dysregulation as a pivotal pathogenic mechanism in AD and highlight KIN as a promising therapeutic candidate by targeting microglial IDH1 to restore metabolic and functional homeostasis.

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Organizational Affiliation: 
• The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, China.
Department of Neurology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China.
NHC Key Laboratory of Neurodegenerative diseases (University of South China), Hengyang, China.
Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, China.
Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangdong-Hong Kong Joint Laboratory for Psychiatric Disorders, Guangdong Province Key Laboratory of Psychiatric Disorders, Guangdong Basic Research Center of Excellence for Integrated Traditional and Western Medicine for Qingzhi Diseases, Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China.
School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China.
College of Basic Sciences, College of Basic Sciences, Shanxi Agricultural University, Jinzhong, China.
Key Laboratory of Clinical Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, Hebei, China.
The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation Method to Treat Multiple Sclerosis of State Administration of Traditional Chinese Medicine/Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, China.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 100.18 kDa 
• Atom Count: 6,550 
• Modeled Residue Count: 822 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	443	Homo sapiens	Mutation(s): 0  Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874  Go to UniProtKB:  O75874
PHAROS:  O75874 GTEx:  ENSG00000138413

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EOQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	Kinsenoside C10 H16 O8 MQEPWBMWFIVRPS-ZGSHZZHUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free:  0.301 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.899	α = 90
b = 112.379	β = 91.88
c = 97.766	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Ouyang, S., Zhao, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82172287

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Database references