Highly Selective c-Jun N-Terminal Kinase (JNK) 2 and 3 Inhibitors with In Vitro CNS-like Pharmacokinetic Properties

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Highly selective c-Jun N-terminal kinase (JNK) 2 and 3 inhibitors with in vitro CNS-like pharmacokinetic properties prevent neurodegeneration.

Probst, G.D.Bowers, S.Sealy, J.M.Truong, A.P.Hom, R.K.Galemmo, R.A.Konradi, A.W.Sham, H.L.Quincy, D.A.Pan, H.Yao, N.Lin, M.Toth, G.Artis, D.R.Zmolek, W.Wong, K.Qin, A.Lorentzen, C.Nakamura, D.F.Quinn, K.P.Sauer, J.M.Powell, K.Ruslim, L.Wright, S.Chereau, D.Ren, Z.Anderson, J.P.Bard, F.Yednock, T.A.Griswold-Prenner, I.

(2011) Bioorg Med Chem Lett 21: 315-319

  • DOI: https://doi.org/10.1016/j.bmcl.2010.11.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In this Letter, we describe the discovery of selective JNK2 and JNK3 inhibitors, such as 10, that routinely exhibit >10-fold selectivity over JNK1 and >1000-fold selectivity over related MAPKs, p38α and ERK2. Substitution of the naphthalene ring affords an isoform selective JNK3 inhibitor, 30, with approximately 10-fold selectivity over both JNK1 and JNK2. A naphthalene ring penetrates deep into the selectivity pocket accounting for the differentiation amongst the kinases. Interestingly, the gatekeeper Met146 sulfide interacts with the naphthalene ring in a sulfur-π stacking interaction. Compound 38 ameliorates neurotoxicity induced by amyloid-β in human cortical neurons. Lastly, we demonstrate how to install propitious in vitro CNS-like properties into these selective inhibitors.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, United States. gary.probst@elan.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10362Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 589

Download Ideal Coordinates CCD File 
B [auth A]5-[2-(cyclohexylamino)pyridin-4-yl]-4-naphthalen-2-yl-2-(tetrahydro-2H-pyran-4-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one
C28 H31 N5 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
589 PDBBind:  3OY1 IC50: 16 (nM) from 1 assay(s)
Binding MOAD:  3OY1 IC50: 16 (nM) from 1 assay(s)
BindingDB:  3OY1 IC50: min: 16, max: 420 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.126α = 90
b = 71.328β = 90
c = 107.752γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Database references, Derived calculations