9Z3C | pdb_00009z3c

Human ClpP with drug

• PDB DOI: https://doi.org/10.2210/pdb9Z3C/pdb

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


• Deposited: 2025-11-06 Released: 2026-09-16 
• Deposition Author(s): Majaesic, E., Barghash, M., Lee, J., Houry, W.A.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Dysregulation of Human ClpP Using Small Molecules with Piperazine-Based Scaffold for Diffuse Intrinsic Pontine Glioma Therapy Validated by Patient-Derived Tumor Organoids.

Miciaccia, M., Armenise, D., Baldelli, O.M., Liturri, A., Mammone, M., Graziano, G., Contino, M., Rizzo, F., Polosa, P.L., Bruni, F., Deligne, C., Broutier, L., Cavallaro, G., Fortuna, C.G., Tolomeo, A., Green, C., Bonifazi, A., Majaesic, E.M., Barghash, M.M., Josh Lee, N.P., Gratteri, C., Talarico, C., Filieri, S., Micalizzi, G., Donnarumma, D., Dugo, P., Mondello, L., Sardanelli, A.M., Houry, W.A., Nazarian, J., Ferorelli, S., Perrone, M.G., Scilimati, A.

(2026) J Med Chem 69: 18386-18413

• PubMed: 42418817 
• DOI: https://doi.org/10.1021/acs.jmedchem.6c00777
• Primary Citation Related Structures: 
  9Z3C


• PubMed Abstract: 
  

  Diffuse intrinsic pontine glioma (DIPG) is a dismal pediatric brainstem tumor with a median survival of approximately 12 months and no curative treatments. ONC201, the most clinically characterized small-molecule, selectively activates human caseinolytic protease P (hClpP). Guided by X-ray structure of the hClpP:ONC201 complex, piperazine-based derivatives were designed and identified compound 26 (DA29) as a lead. Structural studies confirmed its binding to the enzyme hydrophobic allosteric pocket, a finding consistent with its strong proteolytic activation. Permeability under dynamic flow conditions suggested the ability of 26 (DA29) to cross cellular barriers, indicating potential brain tumor penetration. Mechanistically, 26 (DA29) activates hClpP, displaces hClpX from the hClpXP complex, induces mitochondrial dysfunction and ROS accumulation, and exerts cytotoxic effects in patient-derived DIPG cells and organoids. Notably, unlike ONC201, it does not interact with D2/D3 dopamine receptors. Overall, these findings establish a new structural framework for hClpP-targeted therapies and support further development of 26 (DA29) for DIPG treatment.

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Organizational Affiliation: 
• Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", 70125Bari, Italy.
Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", 70125Bari, Italy.
Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", 70125Bari, Italy.
Childhood cancers and Cell states Team (C3 team), Consortium South-ROCK, LabEx DEVweCAN, Institut Convergence Plascan, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, 69008Lyon, France.
Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, 95125Catania, Italy.
ITELPHARMA, ITEL Telecomunicazioni S.R.L., 70037Ruvo di Puglia (Bari), Italy.
Department of Pharmacology and Toxicology, Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, Texas77555, United States.
Department of Chemistry, University of Toronto, 80 St. George Street, OntarioM5S 3H6Toronto, Canada.
Department of Biochemistry, University of Toronto, 661 University Avenue, OntarioM5G 1M1Toronto, Canada.
LIGHT S.c.a.r.l., 25123Brescia, Italy.
Dompé Farmaceutici SpA, EXSCALATE, I-80131Napoli, Italy.
Department of Translational Biomedicine and Neuroscience, University of Bari "Aldo Moro", 70124Bari, Italy.
Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale G. Palatucci 13, 98168Messina, Italy.
Chromaleont s.r.l., c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale G. Palatucci 13, 98168Messina, Italy.
Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8008Zurich, Switzerland.

Biological Assembly 1  

Global Symmetry: Dihedral - D7  (Explore in 3D)
Global Stoichiometry: Homo 14-mer - A14 

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

Macromolecule Content 

• Total Structure Weight: 172.34 kDa 
• Atom Count: 9,818 
• Modeled Residue Count: 1,223 
• 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
PHAROS:  Q16740 GTEx:  ENSG00000125656

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CZ5( Subject of Investigation/LOI)	H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], N [auth F], O [auth G]	4-{[3-(trifluoromethyl)phenyl]methyl}-1-{[4-(trifluoromethyl)phenyl]methyl}piperazin-2-one C20 H18 F6 N2 O FMSMCCDRQVHJID-UHFFFAOYSA-N
GOL	M [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.061	α = 90
b = 121.139	β = 116.58
c = 100.826	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Majaesic, E., Barghash, M., Lee, J., Houry, W.A.

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

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release