Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42597.66 
• Atom Count: 2818 
• Residue Count: 364 
• Unique protein chains: 1

2ZDT

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

• DOI: 10.2210/pdb2ZDT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2007-11-27 Released: 2008-09-23 
• Deposition Author(s): Sogabe, S., Asano, Y., Fukumoto, S., Habuka, N., Fujishima, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.262 
• R-Value Work: 0.216 

Literature

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

• PubMed: 18313930 
• DOI: 10.1016/j.bmc.2008.02.028


• 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.

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Organizational Affiliation: 

Medicinal Chemistry Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company, Ltd, 17-85, Jusohonmachi 2-chome, Osaka 532-8686, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Mitogen-activated protein kinase 10	A	364	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10 (JNK3, JNK3A, PRKM10, SAPK1B) EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens) Go to Gene View: MAPK10 Go to UniProtKB:  P53779

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
46C	A	4-[(6-chloro-1-oxo-4-phenyl-3-propanoylisoquinolin-2(1H)-yl)methyl]benzoic acid C26 H20 Cl N O4 ITAZALHTZBIKDO-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
46C	IC50: 9.6 - 2300 nM (93) BINDINGDB
46C	IC50: 9.6 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.262 
• R-Value Work: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.331	α = 90.00
b = 71.687	β = 90.00
c = 108.103	γ = 90.00

Software Package:

Software Name	Purpose
d*TREK	data reduction
AMoRE	phasing
CNX	refinement
d*TREK	data scaling
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-27 
• Released Date: 2008-09-23 
• Deposition Author(s): Sogabe, S., Asano, Y., Fukumoto, S., Habuka, N., Fujishima, A.

Revision History 

• Version 1.0: 2008-09-23
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Non-polymer description, Version format compliance