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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9XYH

This is version 1.0 of the entry. See complete history.

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

DOI: https://doi.org/10.1038/s41467-026-78140-5

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

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit, mitochondrial	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16740
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CRQ( Subject of Investigation/LOI) Query on A1CRQ Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth D]	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		Interactions Focus chain H [auth A] Focus chain I [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth D]

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release