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

Experimental Data Snapshot

  • Resolution: 2.28 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.189 

Starting Model: experimental
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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: https://doi.org/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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10353Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on JK1

Download Ideal Coordinates CCD File 
B [auth A]3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-1-yl}-N-(3,4,5-trimethoxyphenyl)benzamide
C26 H25 N5 O5
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on OCY
Binding Affinity Annotations 
IDSourceBinding Affinity
JK1 PDBBind:  3FI2 IC50: 25 (nM) from 1 assay(s)
BindingDB:  3FI2 IC50: min: 25, max: 1200 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.28 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.694α = 90
b = 124.525β = 90
c = 69.012γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description