3FI2

Crystal structure of JNK3 with amino-pyrazole inhibitor, SR-3451


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.180 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 10
A
353Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
JK1
Query on JK1

Download SDF File 
Download CCD File 
A
3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-1-yl}-N-(3,4,5-trimethoxyphenyl)benzamide
3-(4-(3-phenylureido)-1H-pyrazol-1-yl)-N-(3,4,5-trimethoxyphenyl)benzamide
C26 H25 N5 O5
RQEFLPVRZJPIAZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
OCY
Query on OCY
A
L-PEPTIDE LINKINGC5 H11 N O3 SCYS
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JK1IC50: 25 - 1200 nM (95) BINDINGDB
JK1IC50: 25 nM BINDINGMOAD
JK1IC50: 25 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.694α = 90.00
b = 124.525β = 90.00
c = 69.012γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
PHENIXmodel building
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-10 
  • Released Date: 2009-03-03 
  • Deposition Author(s): Habel, J.E.

Revision History 

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