Structural insights into the ATP binding pocket of the anaplastic lymphoma kinase by site-directed mutagenesis, inhibitor binding analysis, and homology modeling

J Med Chem. 2006 Sep 21;49(19):5759-68. doi: 10.1021/jm060380k.


Anaplastic lymphoma kinase (ALK) is a valid target for anticancer therapy; however, potent ALK inhibitors suitable for clinical use are lacking. Because the majority of described kinase inhibitors bind in the ATP pocket of the kinase domain, we have characterized this pocket in ALK using site-directed mutagenesis, inhibition studies, and molecular modeling. Mutation of the gatekeeper residue, a key structural determinant influencing inhibitor binding, rendered the fusion protein, NPM/ALK, sensitive to inhibition by SKI-606 in the nanomolar range, while PD173955 inhibited the NPM/ALK mutant at micromolar concentrations. In contrast, both wild type and mutant NPM/ALK were insensitive to imatinib. Computer modeling indicated that docking solutions obtained with a homology model representing the intermediate conformation of the ALK kinase domain reflected closely experimental data. The good agreement between experimental and virtual results indicate that the ALK molecular models described here are useful tools for the rational design of ALK selective inhibitors. In addition, 4-phenylamino-quinoline compounds may have potential as templates for ALK inhibitors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry*
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Anaplastic Lymphoma Kinase
  • Aniline Compounds / chemistry
  • Aniline Compounds / pharmacology
  • Benzamides
  • Binding Sites
  • Catalytic Domain
  • Cells, Cultured
  • Computer Simulation
  • Humans
  • Imatinib Mesylate
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Nitriles / chemistry
  • Nitriles / pharmacology
  • Piperazines / chemistry
  • Piperazines / pharmacology
  • Point Mutation
  • Protein Conformation
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / pharmacology
  • Protein-Tyrosine Kinases / antagonists & inhibitors*
  • Protein-Tyrosine Kinases / chemistry*
  • Protein-Tyrosine Kinases / genetics
  • Pyridones / chemistry
  • Pyridones / pharmacology
  • Pyrimidines / chemistry
  • Pyrimidines / pharmacology
  • Quinolines / chemistry
  • Quinolines / pharmacology
  • Receptor Protein-Tyrosine Kinases
  • Sequence Homology, Amino Acid


  • Aniline Compounds
  • Benzamides
  • Nitriles
  • PD 173955
  • Piperazines
  • Protein Kinase Inhibitors
  • Pyridones
  • Pyrimidines
  • Quinolines
  • bosutinib
  • Imatinib Mesylate
  • Adenosine Triphosphate
  • ALK protein, human
  • Anaplastic Lymphoma Kinase
  • Protein-Tyrosine Kinases
  • Receptor Protein-Tyrosine Kinases