7VP9

Crystal structure of human ClpP in complex with ZG111


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Aberrant human ClpP activation disturbs mitochondrial proteome homeostasis to suppress pancreatic ductal adenocarcinoma.

Wang, P.Zhang, T.Wang, X.Xiao, H.Li, H.Zhou, L.L.Yang, T.Wei, B.Zhu, Z.Zhou, L.Yang, S.Lu, X.Zhang, Y.Huang, Y.Gan, J.Yang, C.G.

(2022) Cell Chem Biol 29: 1396-1408.e8

  • DOI: https://doi.org/10.1016/j.chembiol.2022.07.002
  • Primary Citation of Related Structures:  
    7VP9

  • PubMed Abstract: 

    The mitochondrial caseinolytic protease P (ClpP) is a target candidate for treating leukemia; however, the effects of ClpP modulation on solid tumors have not been adequately explored. Here, we report a potent activator of ClpP with the therapeutic potential for pancreatic ductal adenocarcinoma (PDAC). We first validated that aberrant ClpP activation leads to growth arrest of PDAC cells and tumors. We then performed high-throughput screening and synthetic optimization, from which we identified ZG111, a potent activator of ClpP. ZG111 binds to ClpP and promotes the ClpP-mediated degradation of respiratory chain complexes. This degradation activates the JNK/c-Jun pathway, induces the endoplasmic reticulum stress response, and consequently causes the growth arrest of PDAC cells. ZG111 also produces inhibitory effects on tumor growth in cell line-derived and patient-derived xenograft mouse models. Altogether, our data demonstrate a promising therapeutic strategy for PDAC suppression through the chemical activation of ClpP.


  • Organizational Affiliation

    State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7SR (Subject of Investigation/LOI)
Query on 7SR

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
EA [auth I]
FA [auth I]
IA [auth K]
AA [auth G],
CA [auth H],
EA [auth I],
FA [auth I],
IA [auth K],
JA [auth K],
LA [auth L],
O [auth A],
OA [auth N],
P [auth A],
R [auth B],
U [auth D],
V [auth D],
X [auth E]
(6S,9aS)-N-[(4-bromophenyl)methyl]-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide
C30 H33 Br N4 O3
XXPDBCOMEKQMAR-GFNGZDJJSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
GA [auth I]
HA [auth J]
KA [auth K]
BA [auth G],
DA [auth H],
GA [auth I],
HA [auth J],
KA [auth K],
MA [auth L],
NA [auth M],
PA [auth N],
Q [auth A],
S [auth B],
T [auth C],
W [auth D],
Y [auth E],
Z [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.806α = 90
b = 97.408β = 90.63
c = 146.686γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
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

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2022-09-28
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description