Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 

Starting Model: experimental
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Discovery, synthesis and biological evaluation of isoquinolones as novel and highly selective JNK inhibitors (2)

Asano, Y.Kitamura, S.Ohra, T.Itoh, F.Kajino, M.Tamura, T.Kaneko, M.Ikeda, S.Igata, H.Kawamoto, T.Sogabe, S.Matsumoto, S.Tanaka, T.Yamaguchi, M.Kimura, H.Fukumoto, S.

(2008) Bioorg Med Chem 16: 4699-4714

  • DOI: https://doi.org/10.1016/j.bmc.2008.02.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    3-Metoxycarbonyl isoquinolone derivative 1 has been identified as a potent JNK inhibitor and significantly inhibited cardiac hypertrophy in a rat pressure-overload model. Herein, a series of isoquinolones with an imidazolylmethyl or a pyrazolylmethyl group at the 2-position were designed based on X-ray crystallographic analysis of the complex between the isoquinolone compound and JNK3, as wells as the relationship between compound lipophilicity (logD) and activity in a cell-based assay. The compounds prepared showed potent JNK1 inhibitory activities in a cell-based assay. Among them the isoquinolone derivative possessing 5-[(cyclopropylamino)carbonyl]-1-methyl-1H-pyrazole (16e) exhibited significant anti-hypertrophic activity at doses of more than 1mg/kg (po) in a pressure-overload model.

  • Organizational Affiliation

    Medicinal Chemistry Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, 17-85, Jusohonmachi 2-chome, Osaka 532-8686, Japan. Asano_Yasutimi@takeda.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10364Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 46C

Download Ideal Coordinates CCD File 
B [auth A]4-[(6-chloro-1-oxo-4-phenyl-3-propanoylisoquinolin-2(1H)-yl)methyl]benzoic acid
C26 H20 Cl N O4
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
46C BindingDB:  2ZDT IC50: min: 9.6, max: 2300 (nM) from 2 assay(s)
PDBBind:  2ZDT IC50: 9.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.331α = 90
b = 71.687β = 90
c = 108.103γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description