3OXI

Design and Synthesis of Disubstituted Thiophene and Thiazole Based Inhibitors of JNK for the Treatment of Neurodegenerative Diseases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and synthesis of disubstituted thiophene and thiazole based inhibitors of JNK.

Hom, R.K.Bowers, S.Sealy, J.M.Truong, A.P.Probst, G.D.Neitzel, M.L.Neitz, R.J.Fang, L.Brogley, L.Wu, J.Konradi, A.W.Sham, H.L.Toth, G.Pan, H.Yao, N.Artis, D.R.Quinn, K.Sauer, J.M.Powell, K.Ren, Z.Bard, F.Yednock, T.A.Griswold-Prenner, I.

(2010) Bioorg Med Chem Lett 20: 7303-7307

  • DOI: https://doi.org/10.1016/j.bmcl.2010.10.066
  • Primary Citation of Related Structures:  
    3OXI

  • PubMed Abstract: 

    From high throughput screening, we discovered compound 1, the prototype for a series of disubstituted thiophene inhibitors of JNK which is selective towards closely related MAP kinases p38 and Erk2. Herein we describe the evolution of these compounds to a novel class of thiophene and thiazole JNK inhibitors that retain favorable solubility, permeability, and P-gp properties for development as CNS agents for treatment of neurodegeneration. Compound 61 demonstrated JNK3 IC(50)=77 nM and retained the excellent broad kinase selectivity observed for the series.


  • Organizational Affiliation

    Department of Chemical Sciences, Elan Pharmaceuticals, South San Francisco, CA 94080, USA. roy.hom@elan.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 10362Homo 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 8 interacting protein 1B [auth J]10Homo sapiensMutation(s): 0 
Gene Names: MAPK8IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQF2 (Homo sapiens)
Explore Q9UQF2 
Go to UniProtKB:  Q9UQF2
PHAROS:  Q9UQF2
GTEx:  ENSG00000121653 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQF2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SYY
Query on SYY

Download Ideal Coordinates CCD File 
C [auth A]methyl 3-[(thiophen-2-ylacetyl)amino]thiophene-2-carboxylate
C12 H11 N O3 S2
CXOCENPNQSXLGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SYY PDBBind:  3OXI IC50: 2200 (nM) from 1 assay(s)
BindingDB:  3OXI IC50: min: 1600, max: 2.30e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.02α = 90
b = 78.081β = 90
c = 83.514γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations