Surface charge of the β-FXIIa protease domain. (A) Solid surface colored according to the electrostatic potential calculated from the crystal structure of β-FXIIa in complex with compound 1. Positive surface is shown in blue and negative is in red. Some surface loops surrounding the active site cleft and positions of the substrate-binding sites (S4-S4′) are labeled. Noncovalent inhibitors, sugar residues, and sulfate ions are shown as sticks. (B) Thrombin surface charge was calculated from the crystal structure (PDB code 4UFD) of the enzyme in complex with the benzamidine-containing moiety. The inhibitor is shown in green sticks and the view of the thrombin molecule is that of the β-FXIIa molecule orientation shown in panel A. (C) Close-up stereo view of the FXIIa substrate from P3 to P4′ (ball and stick in cyan) interacting with the surface of the substrate-binding area. The residues P3 to P4′ modeled into the active site (see “Materials and methods”) according to the canonical conformation are Lys-Pro-Arg-Ile-Val-Gly-Gly from the FXI amino acid sequence (residues 385-391; the scissile peptide bond is between the underlined residues). The positions of several FXIIa catalytic domain residues, which can form hypothetical interactions with the substrate in the encounter complex are indicated.