Structural Characterization of Kinase Domains

The X-ray crystal structures of the human kinases JAK2 (PDB code: 4ZIM) [53 (link)], FLT3 (PDB code: 4XUF) [54 (link)], EphB (PDB code: 3ZEW [55 (link)], ABL1 (PDB code: 4WA9) [56 (link)], TIE2 (PDB code: 2WQB) [57 (link)], GSK-3β (PDB code: 3ZRK) [58 (link)], and PLK1 (PDB code: 3THB) [59 (link)], were retrieved from the Protein Data Bank [60 ]. The kinase domain for each protein was prepared using the Protein Preparation Wizard of the Schrödinger molecular modeling suite [61 (link)]. Protein structures were reprocessed by assigning bond orders, adding hydrogens, creating disulfide bonds and optimizing H-bonding networks using PROPKA (Jensen Research Group, Copenhagen, Denmark). Finally, energy minimization with a root mean square deviation (RMSD) value of 0.30 Å was applied using an Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, NY, USA) force field.