ABSTRACT Azadirachtaindica (Neem) is a medicinal plant known for its anticancer, antimicrobial, and antioxidant properties. This study evaluated five Neem-derived proteins Cytochrome P450 (full and partial forms), Squalene Epoxidase 1, Cytochrome f (chloroplast), and a Putative LOV Domain-Containing Protein for potential anticancer activity using in silico methods. Proteins were isolated and characterized through SDS-PAGE and MALDI-TOF/TOF mass spectrometry, followed by 3D structural modelling via SWISS-MODEL. Model validation using PROCHECK assessed Ramachandran plots, rotamer outliers, and clash scores to ensure stereochemical accuracy. Molecular docking was performed against two cancer-associated targets, Cyclin-Dependent Kinases (CDKs) and tubulin, using ZDOCK 3.0.2. The Putative LOV Domain-Containing Protein showed the strongest affinity for CDK, forming 43 amino acid interactions with a binding energy of −45,752.6 kJ/mol. Residues such as THR14, LYS34, GLU15, ASP14, HIS162, SER208, GLU209, PRO62, TYR7, TYR8, TYR248, ALA115, ASN245, MET324, and LEU237 contributed to extensive hydrogen bonding and electrostatic networks, suggesting effective suppression of CDK-mediated cell-cycle progression. Squalene Epoxidase 1 displayed dual-target activity, interacting with 31 CDK residues (−69,219.0 kJ/mol) and 41 tubulin residues (−53,204.0 kJ/mol). Key contacts including PRO40, HIS205, GLY206, ARG71, SER230, TYR66, GLU70, and ARG73 indicate potential disruption of kinase signalling and microtubule polymerization. Cytochrome P450 (full length) also showed high affinity toward tubulin, forming 41 interactions (−51,616.0 kJ/mol) primarily through ASN424, ILE788, GLU196, SER795, HIS704, VAL790, TYR867, and ARG868. All complexes demonstrated stability, supported by favourable energy landscapes and low RMSD values (1.2–2.0 Å). Overall, the Putative LOV Domain-Containing Protein, Squalene Epoxidase 1, and Cytochrome P450 emerged as promising candidates for modulating CDK and tubulin activity. These results highlight the potential of Neem-derived proteins as plant-based anticancer agents and provide a foundation for sustainable cancer therapeutics.