title: Cyclin-dependent kinases 5 template: useful for virtual screening.
abstract: The present study reports the development of a template for the active binding site of Cdk5 for structure-based drug design. The developed template of Cdk5 was validated by redocking with ligands I (PBD code 1UNG), II (PBD code 1UNL) and III (PBD code 1UNH). The results demonstrate a good match of the docked and the crystallographic binding orientations with RMSD less than 2.0Å. The validation results show that the constructed Cdk5 template is a good model system for predicting ligand binding orientations and binding affinities. Furthermore, the developed template was applied to predict binding mode and binding affinity of thirty-six known Cdk5 inhibitors. The results showed that the binding energy of almost Cdk5 inhibitors related to their biological evaluation.
authors.affiliation: Natural Products Research Unit, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.
authors.forename: Siripit
authors.initials: S
authors.lastname: Pitchuanchom
authors.forename: Chantana
authors.initials: C
authors.lastname: Boonyarat
authors.forename: Stefano
authors.initials: S
authors.lastname: Forli
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
authors.forename: Chavi
authors.initials: C
authors.lastname: Yenjai
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D051360:Cyclin-Dependent Kinase 5 / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D015195:Drug Design; D006801:Humans; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D047428:Protein Kinase Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D015203:Reproducibility of Results; D013816:Thermodynamics
chemical_list: D008024:Ligands; D047428:Protein Kinase Inhibitors; D051360:Cyclin-Dependent Kinase 5