The metallofullerenol Gd@C82(OH)22 is regarded as a potential anti-tumor therapeutic due to its metastasis inhibition in numerous experiments. As a promising nanodrug, the toxicity of Gd@C82(OH)22 requires thorough assessment before substantial clinical application. In the present study, we focus on the interaction between Gd@C82(OH)22 and the cytochrome P450 (CYP) enzyme CYP2C8. CYP2C8 can metabolize more than 60 clinically-used drugs as well as numerous endogenous compounds and hence is a representative target for nanotoxicity. From all-atom molecular dynamics simulations and free energy calculations, we observe that Gd@C82(OH)22 binds favorably to the B–C and F-G loops that are substrate recognition sites (SRS) in CYPs. Moreover, binding on these two loops blocks the openings of channels 2b, 2e and 4, three of the most common channels that allow substrates to access and egress from the deeply buried heme active site. We find that bindingis largely driven by electrostatic interactions, with the induced negative charge on the surface of Gd@C82(OH)22 interacting favorably with the positively charged B–C and F-G loops and only modestly with the negatively charged K′-L loop.