Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 42.60 kDa 
• Atom Count: 2980 
• Modelled Residue Count: 342 
• Deposited Residue Count: 364 
• Unique protein chains: 1

2ZDT

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

• PDB DOI: 10.2210/pdb2ZDT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.00 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
• Primary Citation of Related Structures:  
  2ZDT


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	364	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
PHAROS:  P53779

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding 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

• Method: X-RAY DIFFRACTION
• 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 = 50.331	α = 90
b = 71.687	β = 90
c = 108.103	γ = 90

Software Package:

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

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
  Changes: Non-polymer description, Version format compliance