9IQQ | pdb_00009iqq

Crystal structure of PKM2 in complex with a natural activator

• PDB DOI: https://doi.org/10.2210/pdb9IQQ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-13 Released: 2025-11-19 
• Deposition Author(s): Chen, T.J., Wang, W.C.
• Funding Organization(s): National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.257 (DCC) 

Starting Model: experimental

Literature

GSH as an A-A Type Allosteric Activator of PKM2: Modulating Cancer Cell Homeostasis and Ferroptosis Susceptibility.

Chen, T.J., Lo, C.J., Wu, M.J., Sit, W.Y., Hsu, H.Y., Huang, Y.C., Lu, C.H., Chen, Y.L., Fang, W.K., Yang, S.M., Chen, P.L., Haraguchi, T., Hiraoka, Y., Lin, C.Y., Cheng, M.L., Yang, M.H., Kung, H.J., Wang, W.C.

(2025) Adv Sci (Weinh) : e19368-e19368

• PubMed: 41215470 
• DOI: https://doi.org/10.1002/advs.202519368
• Primary Citation of Related Structures:  
  9IQQ


• PubMed Abstract: 
  

  This study identifies glutathione (GSH) as an endogenous A-A type allosteric activator of pyruvate kinase M2 (PKM2), stabilizing it in its active tetrameric form through binding at the A-A interface. This PKM2-GSH interaction links GSH metabolism to ferroptosis regulation. Transcriptomic analyses across cancers demonstrate strong correlations between GSH, SLC7A11, PKM2, glycolysis, and ferroptosis pathways. By depleting GSH and activating PKM2, ferroptosis is enhanced in PKM2-dependent cancer models. This approach leads to significant changes in central carbon and lipid metabolism, disrupts mitochondrial function, and drives ferroptotic cell death. The combined treatment markedly suppresses tumor growth in a xenograft model. Elevated PKM2 and SLC7A11 expression levels correlate with poorer survival outcomes, indicating their potential as biomarkers for ferroptosis-based therapy. The findings demonstrate a dual role for GSH in cellular homeostasis and identify the PKM2-GSH-SLC7A11 axis as a therapeutic target for aggressive cancers.

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Organizational Affiliation: 
• Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu, 300044, Taiwan.
Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan.
Metabolomics Core Laboratory, Healthy Aging Research Center, Chang Gung University, Taoyuan, 333323, Taiwan.
Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, 333423, Taiwan.
Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan.
Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 300093, Taiwan.
Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
School of Dentistry, Kaohsiung Medical University, Kaohsiung, 807378, Taiwan.
Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, 333323, Taiwan.
Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 110301, Taiwan.
Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, 95817, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 242.08 kDa 
• Atom Count: 15,854 
• Modeled Residue Count: 2,036 
• Deposited Residue Count: 2,204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate kinase PKM	A, B, C, D	551	Homo sapiens	Mutation(s): 0  Gene Names: PKM, OIP3, PK2, PK3, PKM2 EC: 2.7.1.40 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens) Explore P14618  Go to UniProtKB:  P14618
PHAROS:  P14618 GTEx:  ENSG00000067225

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBP (Subject of Investigation/LOI)	F [auth B], G [auth C], H [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
GSH (Subject of Investigation/LOI)	E [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.264 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.257 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.824	α = 90
b = 130.288	β = 93.969
c = 104.456	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Chen, T.J., Wang, W.C.

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Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	NSC-105-2314-B-007 -001

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release