8WUZ | pdb_00008wuz

Development of 2-imino-2,3,5,6,7,8-hexahydropyrido[4,3-d]pyrimidin-4(1H)-one derivatives as human caseinolytic peptidase P (hClpP) activators


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Development of novel imipridone derivatives with potent anti-cancer activities as human caseinolytic peptidase P (hClpP) activators.

Zhang, Y.Jiang, J.Ding, H.Li, Q.Xiao, Y.Sun, H.

(2024) Bioorg Chem 153: 107765-107765

  • DOI: https://doi.org/10.1016/j.bioorg.2024.107765
  • Primary Citation Related Structures: 
    8WUZ

  • PubMed Abstract: 

    Based on a clinically staged small molecular hClpP activator ONC201, a class of imipridone derivatives was designed and synthesized. These compounds were evaluated in a protease hydrolytic assay, as well as cell growth inhibition assays in three cancer cell lines, MIA PACA-2, HCT116, and MV4-11. A number of compounds that can more potently activate hClpP and more effectively inhibit cell growth in the three cancer cell lines than ONC201 were identified. The most potent compound, ZYZ-17, activated hClpP with an EC 50 value of 0.24 µM and inhibited the growth of the three cancer cell lines with IC 50 values of less than 10 nM. Mechanism studies for ZYZ-17 revealed that it potently activates cellular hClpP, efficiently induces the degradation of hClpP substrates, and robustly induces apoptosis in the three cancer cell lines. Furthermore, ZYZ-17 demonstrated a promising pharmacokinetic (PK) profile and exhibited highly potent in vivo antitumor activity in a pancreatic cancer MIA PACA-2 xenograft model in BALB/c nude mice.


  • Organizational Affiliation
    • Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.

Macromolecule Content 

  • Total Structure Weight: 173.21 kDa 
  • Atom Count: 10,128 
  • Modeled Residue Count: 1,287 
  • Deposited Residue Count: 1,547 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XFU

Query on XFU



Download:Ideal Coordinates CCD File
H [auth A]
J [auth B]
M [auth C]
O [auth D]
Q [auth E]
H [auth A],
J [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G]
5-[(3-fluorophenyl)methyl]-9-[[4-(trifluoromethyl)phenyl]methyl]-1,5,9,11-tetrazatricyclo[8.4.0.0^{2,7}]tetradeca-2(7),10-dien-8-one
C25 H24 F4 N4 O
HVYZWRNDSSHYMR-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
L [auth B]
N [auth C]
P [auth D]
I [auth A],
K [auth B],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.277α = 90
b = 184.938β = 90
c = 163.222γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AUTOMARdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references