Human MDR1 encodes an ATP-binding cassette transporter, P-glycoprotein, that mediates multiple drug resistance (MDR) to antitumor agents. It has been previously shown that photoaffinity drug-labeling sites reside within, or near, the last transmembrane loop of each cassette within P-glycoprotein (transmembrane domains (TM) 5-6 and 11-12). A genetic approach was used to determine if the drug-labeling site in the second cassette contains functionally important amino acids. Since human MDR3 is 77% identical to MDR1 but does not mediate MDR, the region from TM10 to the C terminus of MDR1 was replaced with the corresponding sequences from MDR3. The resultant chimeric protein was expressed but not functional. By using progressively smaller replacements, we show that replacements limited to TM12 markedly impaired resistance to actinomycin D, vincristine, and doxorubicin, but not to colchicine. The phenotype was associated with an impaired ability to photoaffinity label the chimeric P-glycoprotein with [125I]iodoaryl azidoprazosin. In contrast, replacement of the loop between TM11 and 12 appears to create a more efficient drug pump for actinomycin D, colchicine, and doxorubicin, but not vincristine. These results suggest that, similar to voltage-gated ion channels, amino acids within and immediately N-terminal to the last transmembrane domain of P-glycoprotein compose part of the drug-binding pocket and are in close proximity to photoaffinity drug-labeling domains.