Protein　kinase　CK2　has　been　considered　as　an　attractive　therapeutic　target　of　cancer　therapy.　The　tricyclic　quinoline　compound　CX-4945　is　the　first　representative　of　CK2　inhibitors　used　in　human　clinical　trials.　The　binding　of　non-2,6-naphtyridine　substituted　compounds　27e　(IC50　＞　500　nM)　and　27h　(IC50　＞　1000　nM)　to　CK2　is　abolished.　However,　the　unbinding　mechanisms　due　to　the　key　pharmacophore　group　replacement　of　compounds　27e　and　27h　are　unveiled.　In　the　present　work,　combined　computational　analysis　was　performed　to　investigate　the　underlying　structural　basis　of　the　low-affinity　of　two　systems.　As　indicated　in　the　results,　the　loss　of　hydrogen　bonds　between　the　non-2,6-naphtyridine　and　the　hinge　region　destroyed　the　proper　recognition　of　the　two　complexes.　Besides,　the　allosteric　mechanisms　between　the　deviated　ligands　and　the　changed　regions　(G-loop,　C-loop　and　beta　4/beta　5　loop)　are　proposed.　Furthermore,　energetic　analysis　was　evaluated　by　detailed　energy　calculation　and　residue-based　energy　decomposition.　More　importantly,　the　summary　of　known　polar　pharmacophore　groups　elucidates　the　pivotal　roles　of　hinge　region　sub-pocket　in　the　binding　of　CK2　inhibitors.　These　results　provide　rational　clues　to　the　fragment-based　design　of　more　potent　CK2　inhibitors.