Active EGFR-TKD was modelled on the basis of PDB entries 1M17 (which also provided the initial erlotinib conformation) [10 (link)] and 2ITX [11 (link)], and the L834R mutant was modelled on the basis of PDB entry 2ITV [11 (link)]. Inactive EGFR-TKD was modelled based on PDB entries 2GS7 [12 (link)] and 1XKK [13 (link)]. Protein and ligand conformations were prepared using the Protein Preparation Wizard and LigPrep protocols from Schrödinger Software. All docking simulations used the OPLS (Optimized Potentials for Liquid Simulations) force field [30 ], and used Schrödinger's IFD (Induced Fit Docking) package [31 (link)]. Ligand was first docked to rigid protein using Glide XP [32 (link)]. For the resulting top 20 complex conformations, the protein side chains within 5.0 Å of the ligand in that pose were subjected to conformational search and minimized using Prime [33 (link)] and the ligand was redocked to the 20 new receptor conformations.
Protocol detail
Modeling EGFR-TKD Structures and Dynamics
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Other organizations : University of Pennsylvania
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Variable analysis
independent variables
- Protein and ligand conformations
- Protein preparation using the Protein Preparation Wizard
- Ligand preparation using LigPrep protocols
- Docking simulations using the OPLS force field
- Docking simulations using Schrödinger's IFD package
- Ligand docking to rigid protein using Glide XP
- Protein side chain conformational search and minimization using Prime
- Protein-ligand complex conformations
- PDB entries used as the basis for modeling the active EGFR-TKD (1M17, 2ITX, 2ITV) and inactive EGFR-TKD (2GS7, 1XKK)
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