Fig. 1
Structural mode of EC48 binding to FP2. a Molecular structure of the EC48 inhibitor. The different chemical groups of EC48 are demarcated as #1, benzodioxol; #2, ketone; #3, nitrobenzene. b A single FP2 copy from the crystallographic structure, shown in schematic representation (red). EC48 (orange) and the side chains of the catalytic dyad residues (C285, H417) are shown as sticks. c Surface representation of FP2 in the same orientation as panel b. The surface of catalytic site residues is coloured yellow. The substrate-binding cleft is denoted via a dashed line (green). d, e Sections of OMIT-type Fo–Fc electron density maps showing the EC48 binding sites of the two FP2 copies in the crystal, contoured at 3.5 σ. EC48 ligands were absent during OMIT refinement and are shown here for reference. f Superposition of EC48 binding positions in the two FP2 copies in the crystal. g Molecular interactions involved in EC48 binding. The side chains of FP2 residues that form Van der Waals and p-stacking interactions with EC48 are shown as spheres. FP2 residues involved in hydrogen bonding to EC48 are shown as sticks and putative hydrogen bonds are denoted by dashed lines in yellow. h Sequence conservation at the vicinity (< 10 Å distance) of the EC48 binding site, shown in surface representation. FP2 residues conserved in > 50% of human cathepsin sequences in the alignment of Fig. 2 are coloured pink. Residues conserved or similar in > 50% of human cathepsins are coloured light brown. FP2 residues that differ in > 50% of human cathepsins are coloured grey. FP2 residues noted in text for their divergence in cathepsins are labelled