9XYH | pdb_00009xyh

Human mitochondrial ClpP in complex with OICR-18704 in the heptameric state

• PDB DOI: https://doi.org/10.2210/pdb9XYH/pdb
• EM Map EMD-72334: EMDB EMDataResource

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


• Deposited: 2025-08-26 Released: 2026-10-14 
• Deposition Author(s): Uday, A.B., Zeytuni, N., Goncalves, M., Vahidi, S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Allosteric inhibition of human mitochondrial ClpP by hijacking the dordaviprone (ONC201) binding site.

Goncalves, M.M., Uday, A.B., Watson, I.D.G., Chau, A.M., Kalhor-Monfared, S., Wan, B., Kiyota, T., Currie, S.Q.W., Jitkova, Y., Feng, Y., Diamandas, M., Ling, D., Ma, M., Mancini, R.S., Wang, Z., Casas-Selves, M., Joshi, D., Mohammed, M., Subramaniam, R., Fernandes, E.L., Yan, Y., Pomroy, N., Hurren, R., Gronda, M., Velyvis, A., Yudin, A.K., Reed, M.A., Prive, G., Aman, A., Isaac, M., Marcellus, R., Uehling, D., Schimmer, A.D., Zeytuni, N., Vahidi, S.

(2026) Nat Commun 17

• PubMed: 42946762 
• DOI: https://doi.org/10.1038/s41467-026-78140-5
• Primary Citation Related Structures: 
  9XYH, 9XYJ


• PubMed Abstract: 
  

  ClpP protease maintains proteostasis in human mitochondria and is overexpressed in cancers such as acute myeloid leukemia (AML). While activators such as dordaviprone (ONC201) have reached the clinic, the development of ClpP inhibitors has been hampered by paradoxical activation upon orthosteric inhibitor binding. Here, we report a series of quinazolinone-based compounds that allosterically inhibit human ClpP with nanomolar potency. Cryo-EM and H/D exchange mass spectrometry reveal that our lead compound binds sub-stoichiometrically to a distal hydrophobic pocket ~30 Å from the active sites, disrupts a conserved inter-subunit cluster, and induces a conformational change that misaligns the catalytic triad, thereby inactivating ClpP. The binding site of our quinazolinone-based inhibitors partially overlaps with that of the activator dordaviprone. In a xenograft mouse model of leukemia, our lead compound significantly reduced tumor burden following short-term oral administration. Our findings identify a regulatory hotspot in human ClpP and a mechanistically distinct inhibition strategy.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
Ontario Institute for Cancer Research, Toronto, ON, Canada.
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
Department of Chemistry, University of Toronto, Toronto, ON, Canada.
UHN Therapeutics, Krembil Brain Institute, University Health Network, Toronto, ON, Canada.
Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
Ontario Institute for Cancer Research, Toronto, ON, Canada. [e-mail].
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. [e-mail].
Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada. [e-mail].
Centre de Recherche en Biologie Structurale (CRBS), Montréal, QC, Canada. [e-mail].
Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 170.26 kDa 
• Atom Count: 9,084 
• Modeled Residue Count: 1,146 
• Deposited Residue Count: 1,547 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit, mitochondrial	A, B, C, D, E, F, G	221	Homo sapiens	Mutation(s): 0  Gene Names: CLPP EC: 3.4.21.92
UniProt & NIH Common Fund Data Resources
Find proteins for Q16740 (Homo sapiens) Explore Q16740  Go to UniProtKB:  Q16740
GTEx:  ENSG00000125656

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CRQ (Subject of Investigation/LOI)	H [auth A], I [auth D]	4-[4-({7-chloro-3-[(1S)-1-cyanoethyl]-4-oxo-3,4-dihydroquinazolin-2-yl}methyl)piperazin-1-yl]-2-(trifluoromethyl)benzonitrile C24 H20 Cl F3 N6 O BXKKKAXDFWWIBK-HNNXBMFYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Uday, A.B., Zeytuni, N., Goncalves, M., Vahidi, S.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-191940

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release
  
• Version 1.1: 2026-11-11
  Changes: Data collection, Database references