Binding pockets of the two models were analyzed with SiteMap (version 3.7, Schrödinger, LLC, New York, NY, 2015): protein binding site was defined as the region within 10 Å from residue N93, thus the ECL2 region was excluded and the surface differences were due only to different conformations of residues in TM helices.
The binding site was defined on the basis of used reference ligands with a radius of 10 Å.
For each structure, the binding site was defined at 4Å around the co-crystallized ligand for the protomol generation step.
Like in previous work, the binding site was defined as those AAs that differed between the different mutants (a total of 24 residues) [28].
In GOLD, the binding site was defined as a sphere with a radius of 10 Å centered at the position of the Nε atom in residue Gln 257.
In GOLD, the binding site was defined as a sphere with a radius of 10 Å centered at the position of atom C14 in the bound ligand.
In this study, an experimental binding site is defined as the geometric center of a ligand bound to the target protein, whereas the computationally predicted binding pocket center is obtained from eFindSite [9].
In GOLD, the binding site was defined as a sphere with a radius of 10 Å centered at the position of atom C6 in the bound sialic acid ligand.
For each protein, the binding site was defined as a 40 × 40 × 40 Å cube centered on the occupied space of the original ligand with a spacing of 0.375 Å between the grid points.
Using a different docking software (ParaDockS) than in [24], a new CYP 1A2 model was calibrated automatically using the same dataset of compounds and protein structure (for which the center of the binding site was defined automatically based on heme domain coordinates).
