Subpocket locations. Exceptions for anchor residue definition. The definition of the 85 binding site residues in the KLIFS database is based on a multiple sequence alignment, which can have gaps. It was therefore avoided to set residues with a high gap rate among the structures as anchor residue. Furthermore, some coordinates of an amino acid or a single atom may be missing because they could not be resolved by crystallography. If the coordinates of an anchor residue's Cα atom was missing, the following procedure was applied: If possible, the coordinates were replaced with the geometric center of the two neighboring residues' Cα atoms. If one of those was absent as well, the coordinates of the other neighboring residue were used instead. If both adjacent Cα atoms were missing, the structure was discarded (see Allowed subpocket connections. In order to set up the fragment library, first, the connections between the above defined subpockets were investigated. After manual inspection of the typical structure of known kinase inhibitors (type I and I 1 /2 only), eight allowed subpocket connections were identified as schematically depicted in Figure .C. A first investigation of the generated fragments revealed that 95.2% of the molecules comply with this scheme. The remaining 4.8% ligands exhibiting unexpected subpocket connections were manually inspected: For some cases, special rules could be applied to direct fragmentation towards the defined subpocket connections, others were discarded during this analysis step (see "(3) Molecule fragmentation" and Table (B.4)).