3KVX

JNK3 bound to aminopyrimidine inhibitor, SR-3562

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Synthesis, Biological Evaluation, X-ray Structure, and Pharmacokinetics of Aminopyrimidine c-jun-N-terminal Kinase (JNK) Inhibitors

Kamenecka, T., Jiang, R., Song, X., Duckett, D., Chen, W., Ling, Y.Y., Habel, J., Laughlin, J.D., Chambers, J., Figuera-Losada, M., Cameron, M.D., Lin, L., Ruiz, C.H., Lograsso, P.V.

(2010) J.Med.Chem. 53: 419-431

  • DOI: 10.1021/jm901351f

  • PubMed Abstract: 

    • Given the significant body of data supporting an essential role for c-jun-N-terminal kinase (JNK) in neurodegenerative disorders, we set out to develop highly selective JNK inhibitors with good cell potency and good brain penetration properties. The ...

    Given the significant body of data supporting an essential role for c-jun-N-terminal kinase (JNK) in neurodegenerative disorders, we set out to develop highly selective JNK inhibitors with good cell potency and good brain penetration properties. The structure-activity relationships (SAR) around a series of aminopyrimidines were evaluated utilizing biochemical and cell-based assays to measure JNK inhibition and brain penetration in mice. Microsomal stability in three species, P450 inhibition, inhibition of generation of reactive oxygen species (ROS), and pharmacokinetics in rats were also measured. Compounds 9g, 9i, 9j, and 9l had greater than 135-fold selectivity over p38, and cell-based IC(50) values < 100 nM. Moreover, compound 9l showed an IC(50) = 0.8 nM for inhibition of ROS and had good pharmacokinetic properties in rats along with a brain-to-plasma ratio of 0.75. These results suggest that biaryl substituted aminopyrimidines represented by compound 9l may serve as the first small molecule inhibitors to test efficacy of JNK inhibitors in neurodegenerative disorders.

    Organizational Affiliation: 

    Department of Molecular Therapeutics, and Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way A2A, Jupiter, Florida 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 10
A
364Homo sapiensMutation(s): 0 
Gene Names: MAPK10 (JNK3, JNK3A, PRKM10, SAPK1B)
EC: 2.7.11.24
Find proteins for P53779 (Homo sapiens)
Go to Gene View: MAPK10
Go to UniProtKB:  P53779
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMY
Query on FMY
Download SDF File 
Download CCD File 
A
N-[(2Z)-4-(3-fluoro-5-morpholin-4-ylphenyl)pyrimidin-2(1H)-ylidene]-4-(3-morpholin-4-yl-1H-1,2,4-triazol-1-yl)aniline
C26 H27 F N8 O2
AHMHIFXJPSHHPH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCY
Query on OCY
A
L-PEPTIDE LINKINGC5 H11 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMYIC50: 148 nM BINDINGMOAD
FMYIC50: 148 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.362α = 90.00
b = 125.642β = 90.00
c = 68.744γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance