HIV-1 protease (HIV-1 PR) is vital for the maturation of HIV-1 and as such, it is an attractive drug target. The introduction of new mutations in arising variants may alter drug binding efficacy and as a result, the development of improved protease inhibitors is of importance. We conducted molecular simulations to determine how non-active site polymorphisms affect the structure, stability and drug interactions of a novel South African HIV-1 PR. The findings revealed how non-active site mutations decrease the conformational stability of key regions in the protease, which may reduce drug binding and may contribute to drug resistance.