8YLB | pdb_00008ylb

Cocrystal structures of agonists compound 1 with HsClpP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.260 (Depositor), 0.303 (DCC) 
  • R-Value Work: 
    0.207 (Depositor) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Rational Design of a Novel Class of Human ClpP Agonists through a Ring-Opening Strategy with Enhanced Antileukemia Activity.

Xiang, X.Dai, Z.Luo, B.Zhao, N.Liu, S.Sui, J.Huang, J.Zhou, Y.Gu, J.Zhang, J.Yang, T.Bao, R.Luo, Y.

(2024) J Med Chem 67: 6769-6792

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00338
  • Primary Citation Related Structures: 
    8YLB

  • PubMed Abstract: 

    The activation of Homo sapiens Casein lysing protease P (HsClpP) by a chemical or genetic strategy has been proved to be a new potential therapy in acute myeloid leukemia (AML). However, limited efficacy has been achieved with classic agonist imipridone ONC201 . Here, a novel class of HsClpP agonists is designed and synthesized using a ring-opening strategy based on the lead compound 1 reported in our previous study. Among these novel scaffold agonists, compound 7k exhibited remarkably enhanced proteolytic activity of HsClpP (EC 50 = 0.79 ± 0.03 μM) and antitumor activity in vitro (IC 50 = 0.038 ± 0.003 μM). Moreover, the intraperitoneal administration of compound 7k markedly suppressed tumor growth in Mv4-11 xenograft models, achieving a tumor growth inhibition rate of 88%. Concurrently, 7k displayed advantageous pharmacokinetic properties in vivo . This study underscores the promise of compound 7k as a significant HsClpP agonist and an antileukemia drug candidate, warranting further exploration for AML treatment.


  • Organizational Affiliation
    • State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 342.71 kDa 
  • Atom Count: 19,440 
  • Modeled Residue Count: 2,389 
  • Deposited Residue Count: 3,080 
  • 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, H, I, J, K, L, M, N
220Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LZA
(Subject of Investigation/LOI)

Query on A1LZA



Download:Ideal Coordinates CCD File
AA [auth M]
BA [auth N]
O [auth A]
P [auth B]
Q [auth C]
AA [auth M],
BA [auth N],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
5-[(2-methylphenyl)methyl]-11-(phenylmethyl)-2,5,7,11-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),6-dien-8-one
C24 H26 N4 O
CPQVAKZHOMXNHY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.260 (Depositor), 0.303 (DCC) 
  • R-Value Work:  0.207 (Depositor) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.239α = 90
b = 96.742β = 94.44
c = 124.542γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

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: 2024-05-15
    Type: Initial release