B12N12 nanocage was selected as a drug carrier for 5-fluorouracil (5FU). Both compounds were optimized B3LYP/6-31 + G(d) level in the water. Electrophilic/nucleophilic attack regions and the appropriate interaction sites were determined by molecular electrostatic potential (MEP) maps. The possible interaction structure between 5FU and B12N12 nanocage was determined. Additionally, it was determined that five pieces of 5FU were coordinated to BN nanocage step by step. Each compound is characterized as structurally. IR, H-1-, F-9-, B-11-, C-13-, (15) N-, O-17-NMR spectra are calculated and compared with published data. The interaction energies and deformation energies were calculated for each BN-5FU complex. As for the biological application, 5FU and B12N12 nanocage were interacted with vascular endothelial growth factor receptor 2 (VEGFR2), which PDB ID is 2OH4. The possible structure of drugs at pH = 7 +/- 1 was determined. Molecular docking analyses of each drug and its possible structures were performed with 2OH4. It was found that studied compounds interacted with 2OH4. This result implies that the studied compounds can be used as an anti-cancer drug.