3G9N

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

  • Method: X-RAY DIFFRACTION
  • 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


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A365Homo sapiensMutation(s): 0 
Gene Names: JNK3JNK3AMAPK10PRKM10SAPK1B
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens)
Explore P53779 
Go to UniProtKB:  P53779
PHAROS:  P53779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J88 (Subject of Investigation/LOI)
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
SZYREAUDQRVVLV-DAFNUICNSA-N
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-02-13 
  • 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