The molecular docking analysis revealed that the five Danshen compounds—Cryptotanshinone, Dihydrotanshinone I, Tanshinone I, Tanshinone IIa, and Tetrahydrotanshinone—exhibited strong binding affinities across a panel of lipid and atherosclerosis-related protein targets, which are class I HMGCR, class II HMGCR, low-density lipoprotein receptor (LDLR), peroxisome proliferator-activated receptor-α (PPARA), janus kinase2 (JAK2), and receptor for advanced glycation end products (RAGE), with binding energy values consistently lower than −7.4 kcal/mol. This evidence concerns the gene AGER and atherosclerosis.