JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-phenylindolin-2-one

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure-based design and parallel synthesis of N-benzyl isatin oximes as JNK3 MAP kinase inhibitors.

Cao, J.Gao, H.Bemis, G.Salituro, F.Ledeboer, M.Harrington, E.Wilke, S.Taslimi, P.Pazhanisamy, S.Xie, X.Jacobs, M.Green, J.

(2009) Bioorg Med Chem Lett 19: 2891-2895

  • DOI: https://doi.org/10.1016/j.bmcl.2009.03.043
  • Primary Citation of Related Structures:  
    3G90, 3G9L, 3G9N

  • PubMed Abstract: 

    A series of N-benzylated isatin oximes were developed as inhibitors of the mitogen-activated kinase, JNK3. X-ray crystallographic structures aided in the design and synthesis of novel, selective compounds, that inhibit JNK3, but not p38 MAP kinase and provided key insights into understanding the behavior of gatekeeper residue methionine-146 in determining target selectivity for this series.

  • Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10365Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
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 J88

Download Ideal Coordinates CCD File 
B [auth A](3Z)-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-4-phenyl-1H-indole-2,3-dione 3-oxime
C23 H17 F N2 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
J88 PDBBind:  3G9N Ki: 1800 (nM) from 1 assay(s)
BindingDB:  3G9N Ki: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.313α = 90
b = 72.176β = 90
c = 107.489γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2009-02-24 
  • Deposition Author(s): Jacobs, M.D.

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description