Target-specific scoring methods are more commonly used to identify small-molecule inhibitors among compounds docked to a target of interest. Top candidates that emerge from these methods have rarely been tested for activity and specificity across a family of proteins. Here, we dock a chemical library to CaMKIIδ, a member of the Ca2+/calmodulin (CaM)-dependent protein kinase (CaMK) family, and rescore the resulting protein-compound structures using SVMSP, a target-specific method that we previously developed. Among the 35 selected candidates, three hits were identified, such as quinazoline compound 1 (KIN-1), which inhibited CaMKIIδ kinase activity with single-digit micromolar IC50. Activity across the kinome was assessed by profiling analogs of 1, namely 6 (KIN-236), and an analog of hit compound 2 (KIN-15), namely 14 (KIN-332), against 337 kinases. Interestingly, for 6 (KIN-236), CaMKIIδ and homolog CaMKIIγ were among the top 10 targets. Among the top 25 targets of 6 (KIN-236), IC50 values ranged from 5 to 22 μM. Compound 14 (KIN-332) was not specific towards CaMKII kinases, but the compound inhibited two kinases with sub-micromolar IC50s among the top 25. Derivatives of 1 were tested against several kinases including several members of the CaMK family. The data afforded a limited structure-activity relationship study. Molecular dynamics simulations with explicit-solvent followed by end-point MM-GBSA free energy calculations revealed strong engagement of specific residues within the ATP-binding pocket, and also changes in the dynamics as a result of binding. This work suggests that target-specific scoring approaches like SVMSP may hold promise for the identification of small-molecule kinase inhibitors that exhibit some level of specificity towards the target of interest across a large number of proteins.