Medicinal mushrooms represent an important reservoir of structurally diverse metabolites with significant pharmaceutical potential, particularly for anticancer drug discovery. In the present study, an integrated in silico approach was employed to investigate the molecular characteristics and predicted antiproliferative potential of a benzotetraazacyclopentadecine derivative (C₂₅H₂₉IN₆O₄), a nitrogen-containing heterocyclic metabolite identified from the aqueous extract of wild Ganoderma lucidum. Physicochemical characterization revealed a molecular weight of 604.45 Da, a consensus LogP of 3.87, a topological polar surface area of 131.52 Ų, and favorable hydrogen-bonding capacity, indicating structural features suitable for molecular recognition. Drug-likeness evaluation demonstrated compliance with the Veber, Ghose, Egan, and Muegge criteria, with only a single Lipinski violation attributed to molecular weight and a predicted bioavailability score of 0.55. Molecular target prediction identified the epidermal growth factor receptor (EGFR), cyclin-dependent kinase 2 (CDK2), B-cell lymphoma 2 (Bcl-2), and AKT1 kinase as the most probable cancer-associated targets, with prediction probabilities ranging from 0.71 to 0.89. Molecular docking demonstrated strong binding affinities toward these proteins, particularly EGFR (−9.74 kcal mol⁻¹) and CDK2 (−9.08 kcal mol⁻¹), supported by multiple hydrogen bonds and hydrophobic interactions within their active sites. KEGG pathway enrichment further associated the predicted targets with critical oncogenic pathways, including Pathways in cancer, PI3K–Akt signaling, Cell cycle, and Apoptosis, suggesting a multi-target mechanism underlying the metabolite’s predicted antiproliferative activity. These computational findings identify the benzotetraazacyclopentadecine derivative as a promising natural-product scaffold for anticancer drug discovery and provide a scientific basis for subsequent experimental validation.