Table 5.
Interaction data (interface area, number of H-bonds/salt bridges) detected in the crystallographic structures of thrombin complexes with ligands bound at exosite II or at both exosite II and active site. Functional partners, natural inhibitors, and synthetic compounds are highlighted in pink, yellow, and light blue, respectively. Analyses have been conducted using the PISA program [128].
| Ligand (PDB Entry) | Interface Area (Å2) | NHB | NSB |
|---|---|---|---|
| Exosite II | |||
| Fibrinogen γ’ peptide (2hwl) | 782.3 | 15 | 6 |
| Bovine kringle-2 (2hpp) | 795.2 | 15 | 9 |
| Human kringle-2 (2hpq) | 778.1 | 11 | 10 |
| Heparin (1xmn) * | 396.5 | 2 | 5 |
| Heparin (in the presence of antithrombin III) (1tb6) * | 307.9 | 0 | 6 |
| Platelet glycoprotein Ibα-GPIbα (1p8v) | 934.0 | 11 | 5 |
| Toggle-25t/AF113-18 (5do4) * | 924.9 | 17 | 0 |
| HD22_27mer (4i7y) | 1079.5 | 18 | 0 |
| Suramin (2h9t) | 476.0 | 3 | 0 |
| Exosite II + active site | |||
| Hemadin (1e0f) | 1216.0 | 19 | 7 |
| Madanin-1 (5l6n) | 1365.3 | 24 | 13 |
| Tsetse thrombin inhibitor (6tkl) | 1652.4 | 27 | 11 |
* PDB entries that were manually curated for the analyses.