The chemical modification of lysine residues in human alpha-thrombin has been used to study the interaction of thrombin with human platelets. Phosphopyridoxylation of thrombin using pyridoxal 5'-phosphate (pyridoxal-P) has been shown to inhibit the fibrinogen clotting activity of thrombin but not the catalytic activity (Griffith, M. J. J. Biol. Chem. 254, 3401-3406). Phosphopyridoxylation resulted in marked inhibition of the platelet-activating activity of thrombin. The concentration of pyridoxal-P-thrombin required to induce half-maximal platelet aggregation and release was 60 times greater than that of unmodified thrombin. Binding studies using pyridoxal-P-125I-thrombin showed a loss of both high and low affinity binding of thrombin to the surface of intact gel filtered platelets. In contrast, thrombin modified with pyridoxal-P in the presence of heparin incorporated up to 1 mol of pyridoxal-P per mol of thrombin. The heparin-protected pyridoxal-P-thrombin was only slightly inhibited in its interaction with platelets, and binding studies with the heparin-protected pyridoxal-P-125I-thrombin showed selective loss of low affinity binding but preservation of high affinity binding. These results provide further support for the hypothesis that residues at the macromolecular binding site of thrombin are involved in the binding of thrombin to platelets and further separate this functional region of thrombin into two lysine-containing subregions, one which is protected from modification by heparin which is involved in high affinity binding, and another which is not protected by heparin which is involved in low affinity binding.