8I7X

Crystal structure of human ClpP in complex with ZG36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


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Literature

Assessment of the structure-activity relationship and antileukemic activity of diacylpyramide compounds as human ClpP agonists.

Zhang, R.Wang, P.Wei, B.Chen, L.Song, X.Pan, Y.Li, J.Gan, J.Zhang, T.Yang, C.G.

(2023) Eur J Med Chem 258: 115577-115577

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115577
  • Primary Citation of Related Structures:  
    8I7X

  • PubMed Abstract: 

    Human caseinolytic protease P (ClpP) is required for the regulatory hydrolysis of mitochondrial proteins. Allosteric ClpP agonists dysfunctionally activate mitochondrial ClpP in antileukemic therapies. We previously developed ZG111, a potent ClpP agonist derived from ICG-001, inhibits the proliferation of pancreatic ductal adenocarcinoma cell lines in vitro and in vivo by degrading respiratory chain complex proteins. Herein, we studied the structure-activity relationships of ICG-001 analogs as antileukemia agents. Compound ZG36 exhibited improved stabilization effects on the thermal stability of ClpP in acute myeloid leukemia (AML) cell lines compared with the stabilization effects of ZG111, indicating a direct binding between ZG36 and ClpP. Indeed, the resolved ZG36/ClpP structural complex reveals the mode of action of ZG36 during ClpP binding. Compound ZG36 nonselectively degrades respiratory chain complexes and decreases the mitochondrial DNA, eventually leading to the collapse of mitochondrial function and leukemic cell death. Finally, ZG36 treatment inhibited 3-D cell growth in vitro and suppressed the tumorigenesis of AML cells in xenografted mice models. Collectively, we developed a new class of human ClpP agonists that can be used as potential antileukemic therapies.


  • Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; 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
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
GTEx:  ENSG00000125656 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16740
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OSR (Subject of Investigation/LOI)
Query on OSR

Download Ideal Coordinates CCD File 
AA [auth L]
BA [auth M]
O [auth B]
P [auth B]
Q [auth C]
AA [auth L],
BA [auth M],
O [auth B],
P [auth B],
Q [auth C],
R [auth D],
S [auth F],
T [auth G],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth K]
(6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
C31 H35 Br N4 O4
ZFXGQLLQQPADFS-XHGLXQHVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.24α = 90
b = 96.08β = 92.72
c = 127γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
autoPROCdata 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

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release