3G90

JNK-3 bound to (Z)-5-fluoro-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)indolin-2-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10A [auth X]365Homo sapiensMutation(s): 0 
Gene Names: JNK3JNK3AMAPK10PRKM10
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
GTEx:  ENSG00000109339 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53779
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J72
Query on J72

Download Ideal Coordinates CCD File 
B [auth X](3E)-5-fluoro-1-[(6-fluoro-4H-1,3-benzodioxin-8-yl)methyl]-1H-indole-2,3-dione 3-oxime
C17 H12 F2 N2 O4
DXIHOIDYHQSQKJ-HMMYKYKNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J72 PDBBind:  3G90 Ki: 440 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.655α = 90
b = 72.289β = 90
c = 107.189γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations