8HGK

Crystal structure of human ClpP in complex with ZK53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Selective activator of human ClpP triggers cell cycle arrest to inhibit lung squamous cell carcinoma.

Zhou, L.L.Zhang, T.Xue, Y.Yue, C.Pan, Y.Wang, P.Yang, T.Li, M.Zhou, H.Ding, K.Gan, J.Ji, H.Yang, C.G.

(2023) Nat Commun 14: 7069-7069

  • DOI: https://doi.org/10.1038/s41467-023-42784-4
  • Primary Citation of Related Structures:  
    8HGK

  • PubMed Abstract: 

    Chemo-activation of mitochondrial ClpP exhibits promising anticancer properties. However, we are currently unaware of any studies using selective and potent ClpP activators in lung squamous cell carcinoma. In this work, we report on such an activator, ZK53, which exhibits therapeutic effects on lung squamous cell carcinoma in vivo. The crystal structure of ZK53/ClpP complex reveals a π-π stacking effect that is essential for ligand binding selectively to the mitochondrial ClpP. ZK53 features on a simple scaffold, which is distinct from the activators with rigid scaffolds, such as acyldepsipeptides and imipridones. ZK53 treatment causes a decrease of the electron transport chain in a ClpP-dependent manner, which results in declined oxidative phosphorylation and ATP production in lung tumor cells. Mechanistically, ZK53 inhibits the adenoviral early region 2 binding factor targets and activates the ataxia-telangiectasia mutated-mediated DNA damage response, eventually triggering cell cycle arrest. Lastly, ZK53 exhibits therapeutic effects on lung squamous cell carcinoma cells in xenograft and autochthonous mouse models.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit, mitochondrial
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
222Homo 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
GTEx:  ENSG00000125656 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZLL (Subject of Investigation/LOI)
Query on ZLL

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
EA [auth L]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
EA [auth L],
GA [auth N],
O [auth A],
P [auth A],
R [auth C],
S [auth D],
T [auth E],
V [auth F],
X [auth G],
Z [auth H]
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide
C19 H20 Br F2 N3 O
HRSJZGGIFGZVFD-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
FA [auth M],
Q [auth A],
U [auth E],
W [auth F],
Y [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.31α = 90
b = 97β = 93.98
c = 123.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22037007
National Natural Science Foundation of China (NSFC)China21725801
National Natural Science Foundation of China (NSFC)China22107109
Ministry of Science and Technology (MoST, China)China2022YFC2804104

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references