Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.27 kDa 
• Atom Count: 2809 
• Residue Count: 332 
• Unique protein chains: 2

3OXI

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

• DOI: 10.2210/pdb3OXI/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-21 Released: 2011-05-04 
• Deposition Author(s): Hom, R.K., Bowers, S., Sealy, J., Truong, A., Probst, G.D., Neitzel, M., Neitz, J., Fang, L., Brogley, L., Wu, J., Konradi, A.W., Sham, H., Toth, G., Pan, H., Yao, N., Artis, D.R.

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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 

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

• PubMed: 21071223 
• DOI: 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.

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Organizational Affiliation: 

Department of Chemical Sciences, Elan Pharmaceuticals, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	362	Homo sapiens	Mutation(s): 0  Gene Names: JNK3, JNK3A, MAPK10, PRKM10, SAPK1B EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
NIH Common Fund Data Resources
PHAROS:  P53779 GTEx:  ENSG00000109339

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8 interacting protein 1	J	10	Homo sapiens	Mutation(s): 0  Gene Names: MAPK8IP1, IB1, JIP1, PRKM8IP
Find proteins for Q9UQF2 (Homo sapiens) Explore Q9UQF2  Go to UniProtKB:  Q9UQF2
NIH Common Fund Data Resources
PHAROS:  Q9UQF2 GTEx:  ENSG00000121653

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SYY	A	methyl 3-[(thiophen-2-ylacetyl)amino]thiophene-2-carboxylate C12 H11 N O3 S2 CXOCENPNQSXLGZ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SYY	IC50:  21400   nM  BindingDB
SYY	IC50:  1600   nM  BindingDB
SYY	IC50:  23000   nM  BindingDB
SYY	IC50:  2200   nM  Binding MOAD
SYY	IC50:  1800   nM  BindingDB
SYY	IC50 :  2200   nM  PDBBind
SYY	IC50:  2200   nM  BindingDB

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 = 60.02	α = 90
b = 78.081	β = 90
c = 83.514	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-21 
• Released Date: 2011-05-04 
Deposition Author(s): Hom, R.K., Bowers, S., Sealy, J., Truong, A., Probst, G.D., Neitzel, M., Neitz, J., Fang, L., Brogley, L., Wu, J., Konradi, A.W., Sham, H., Toth, G., Pan, H., Yao, N., Artis, D.R.

Revision History 

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance