2ZDU | pdb_00002zdu

Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2ZDU/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., Ohra, T., Itoh, F., Habuka, N., Fujishima, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.319 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 

Starting Model: experimental

Literature

Discovery, synthesis and biological evaluation of isoquinolones as novel and highly selective JNK inhibitors (1)

Asano, Y., Kitamura, S., Ohra, T., Aso, K., Igata, H., Tamura, T., Kawamoto, T., Tanaka, T., Sogabe, S., Matsumoto, S., Yamaguchi, M., Kimura, H., Itoh, F.

(2008) Bioorg Med Chem 16: 4715-4732

• PubMed: 18313304 
• DOI: https://doi.org/10.1016/j.bmc.2008.02.027
• Primary Citation Related Structures: 
  2ZDU


• PubMed Abstract: 
  

  A novel series of 4-phenylisoquinolones were synthesized and evaluated as c-Jun N-terminal kinase (JNK) inhibitors. Initial modification at the 2- and 3-positions of the isoquinolone ring of hit compound 4, identified from high-throughput screening, led to the lead compound 6b. The optimization was carried out using a JNK1-binding model of 6b and several compounds exhibited potent JNK inhibition. Among them, 11g significantly inhibited cardiac hypertrophy in rat pressure-overload models without affecting blood pressure and the concept of JNK inhibitors as novel therapeutic agents for heart failure was confirmed.

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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]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 42.62 kDa 
• Atom Count: 2,774 
• Modeled Residue Count: 330 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	364	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000109339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
446	B [auth A]	4-[(4-{[6-bromo-3-(methoxycarbonyl)-1-oxo-4-phenylisoquinolin-2(1H)-yl]methyl}phenyl)amino]-4-oxobutanoic acid C28 H23 Br N2 O6 UJOQZQKRUNERFC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
446	BindingDB:  2ZDU	IC50: 9.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.319 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.956	α = 90
b = 70.267	β = 90
c = 107.947	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

• Released Date: 2008-09-23 
Deposition Author(s): Sogabe, S., Ohra, T., Itoh, F., Habuka, N., Fujishima, A.

Revision History  

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