Abstract Protein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-guided atlas of the human and Drosophila kinome, built by applying a new interface-aware scoring framework (iLIS) to AlphaFold-Multimer predictions. The resulting atlas recapitulates hallmark sequence preferences, confirms previously reported and functionally related protein-protein interactions (PPIs), and uncovers previously unrecognized docking interactions. Notably, our analysis predicts a potentially widespread docking motif on homeodomain (HD) transcription factors for interaction with basophilic kinases. We validate selected predictions in cells and in vivo and demonstrate the atlas utility by mechanistically dissecting a key pathway controlling lipid metabolism. This resource provides a blueprint for dissecting signaling networks and for the rational design of docking-site-specific kinase modulators.