Alignment of all docked structures within the thrombin binding site (docked ligands are in green stick representation in A-E).

<p><b>(A)</b> Full view of the binding site. <b>(B)</b> Subsite S₁, residues of the VSWGEGC motif are represented with white spheres, DACE motif is represented as an orange loop, Ser195 is represented with yellow sticks. <b>(C)</b> Subsite S₁, residues of the DACE motif are represented with orange spheres, VSWGEGC motif is represented as a white loop, Ser195 is represented with yellow sticks. <b>(D)</b> Subsite S₂, residues His57, Tyr61, and Trp64 are represented with violet spheres, and residues Trp215 and Gly216 from the VSWGEGC motif are represented with white spheres. <b>(E</b>, <b>F)</b> Subsite S₃, residues of the WRENL motif are represented with brown spheres, residues Trp215 and Glu217 from the VSWGEGC motif are represented with white spheres, and Ile174 is represented with yellow spheres. In f several compounds that have a P₁ moiety with two branches are represented: compounds with two hydrophobic branches are represented with green sticks, and compounds with one of the branches containing a polar group are represented with pink sticks.