These pharmacophores target a highly conserved structural determinant of the ATP binding site in the kinase family, namely an alternating hydrogen bonding pattern present in the so-called hinge peptide portion that connects the N- and C-terminal domain of kinases. Inhibitors form hydrogen bonds with the protein backbone and peripheral groups are oriented towards two hydrophobic pockets called BR-I (binding region-I) and BR-II or towards the phosphate-binding region (PBR). There are two typical inhibitor binding modes, shown in Fig. 9.3, and very often structurally close compounds bind to the ATP site in different topologies and are able to recognize different kinases. For this reason, chemical similarity between kinase inhibitors often fails to correlate with target specificity.

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