3FI3

Crystal structure of JNK3 with indazole inhibitor, SR-3737


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-activity relationships and X-ray structures describing the selectivity of aminopyrazole inhibitors for c-Jun N-terminal kinase 3 (JNK3) over p38.

Kamenecka, T.Habel, J.Duckett, D.Chen, W.Ling, Y.Y.Frackowiak, B.Jiang, R.Shin, Y.Song, X.LoGrasso, P.

(2009) J Biol Chem 284: 12853-12861

  • DOI: 10.1074/jbc.M809430200
  • Primary Citation of Related Structures:  
    3FI2, 3FI3

  • PubMed Abstract: 
  • c-Jun N-terminal kinase 3alpha1 (JNK3alpha1) is a mitogen-activated protein kinase family member expressed primarily in the brain that phosphorylates protein transcription factors, including c-Jun and activating transcription factor-2 (ATF-2) upon ac ...

    c-Jun N-terminal kinase 3alpha1 (JNK3alpha1) is a mitogen-activated protein kinase family member expressed primarily in the brain that phosphorylates protein transcription factors, including c-Jun and activating transcription factor-2 (ATF-2) upon activation by a variety of stress-based stimuli. In this study, we set out to design JNK3-selective inhibitors that had >1000-fold selectivity over p38, another closely related mitogen-activated protein kinase family member. To do this we employed traditional medicinal chemistry principles coupled with structure-based drug design. Inhibitors from the aminopyrazole class, such as SR-3576, were found to be very potent JNK3 inhibitors (IC(50) = 7 nm) with >2800-fold selectivity over p38 (p38 IC(50) > 20 microm) and had cell-based potency of approximately 1 microm. In contrast, indazole-based inhibitors exemplified by SR-3737 were potent inhibitors of both JNK3 (IC(50) = 12 nm) and p38 (IC(50) = 3 nm). These selectivity differences between the indazole class and the aminopyrazole class came despite nearly identical binding (root mean square deviation = 0.33 A) of these two compound classes to JNK3. The structural features within the compounds giving rise to the selectivity in the aminopyrazole class include the highly planar nature of the pyrazole, N-linked phenyl structures, which better occupied the smaller active site of JNK3 compared with the larger active site of p38.


    Organizational Affiliation

    Department of Molecular Therapeutics and Translational Research Institute, The Scripps Research Institute, Jupiter, FL 33458, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A364Homo sapiensMutation(s): 0 
Gene Names: JNK3JNK3AMAPK10PRKM10SAPK1B
EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
NIH Common Fund Data Resources
PHAROS  P53779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JK2
Query on JK2

Download CCD File 
A
3-{5-[(2-fluorophenyl)amino]-1H-indazol-1-yl}-N-(3,4,5-trimethoxyphenyl)benzamide
C29 H25 F N4 O4
GYQLVKWGHKBDMP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCY
Query on OCY
AL-PEPTIDE LINKINGC5 H11 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JK2IC50:  12   nM  Binding MOAD
JK2IC50:  9   nM  BindingDB
JK2IC50 :  12   nM  PDBBind
JK2IC50:  73   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.862α = 90
b = 124.105β = 90
c = 69.519γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance