6DL7

Human mitochondrial ClpP in complex with ONC201 (TIC10)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality.

Ishizawa, J., Zarabi, S.F., Davis, R.E., Halgas, O., Nii, T., Jitkova, Y., Zhao, R., St-Germain, J., Heese, L.E., Egan, G., Ruvolo, V.R., Barghout, S.H., Nishida, Y., Hurren, R., Ma, W., Gronda, M., Link, T., Wong, K., Mabanglo, M., Kojima, K., Borthakur, G., MacLean, N., Ma, M.C.J., Leber, A.B., Minden, M.D., Houry, W., Kantarjian, H., Stogniew, M., Raught, B., Pai, E.F., Schimmer, A.D., Andreeff, M.

(2019) Cancer Cell 35: 721

  • DOI: https://doi.org/10.1016/j.ccell.2019.03.014
  • Primary Citation of Related Structures:  
    6DL7

  • PubMed Abstract: 

    • The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells ...

    The mitochondrial caseinolytic protease P (ClpP) plays a central role in mitochondrial protein quality control by degrading misfolded proteins. Using genetic and chemical approaches, we showed that hyperactivation of the protease selectively kills cancer cells, independently of p53 status, by selective degradation of its respiratory chain protein substrates and disrupts mitochondrial structure and function, while it does not affect non-malignant cells. We identified imipridones as potent activators of ClpP. Through biochemical studies and crystallography, we show that imipridones bind ClpP non-covalently and induce proteolysis by diverse structural changes. Imipridones are presently in clinical trials. Our findings suggest a general concept of inducing cancer cell lethality through activation of mitochondrial proteolysis.

    Organizational Affiliation: 

    The University of Texas MD Anderson Cancer Center, Molecular Hematology and Therapy, Department of Leukemia, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center; Department of Leukemia, Houston, TX 77030, USA. Electronic address: mandreef@mdanderson.org.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit, mitochondrial
A, B, C, D, E, F, G
A, B, C, D, E, F, G
221Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ONC
Query on ONC
Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
J [auth C],
K [auth D],
L [auth E],
H [auth A],
I [auth B],
J [auth C],
K [auth D],
L [auth E],
M [auth F],
N [auth G]
7-benzyl-4-[(2-methylphenyl)methyl]-6,7,8,9-tetrahydroimidazo[1,2-a]pyrido[3,4-e]pyrimidin-5(4H)-one
C24 H24 N4 O
AWBSLIQRVCVMFU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.39α = 90
b = 153.44β = 117.58
c = 104.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references