Table 4.
Interaction data (interface area, number of H-bonds/salt bridges) detected in the crystallographic structures of thrombin complexes with ligands bound at exosite I or at both exosite I 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 I | |||
| Coagulation Factor V (3p6z) | 415.0 | 5 | 4 |
| Human Factor V, A2-B domain linker (3p70) | 297.4 | 2 | 0 |
| Fibrinogen (2a45) | 642.5 | 9 | 2 |
| Platelet glycoprotein Ibα-GPIbα (1ook) | 1060.0 | 17 | 10 |
| Proteinase-activated receptor 1-PAR1 (1nrr) | 401.1 | 4 | 0 |
| Proteinase-activated receptor 3-PAR3 (2pux) | 659.5 | 7 | 4 |
| Thrombomodulin (1dx5) | 772.7 | 12 | 0 |
| Avathrin, C-terminal peptide (5gim) | 516.6 | 3 | 1 |
| IgA fab heavy chain (5e8e) | 526.8 | 5 | 2 |
| Hirugen (1aht) | 627.1 | 7 | 3 |
| Hirullin (1thr) | 727.9 | 10 | 5 |
| Staphylocoagulase (1nu7) | 1661.9 | 22 | 15 |
| Triabin (1avg) | 697.4 | 7 | 5 |
| mTBA (3qlp) | 656.6 | 11 | 0 |
| TBA (4dih) | 565.0 | 12 | 0 |
| TBAΔT12 (4lz1) * | 533.8 | 13 | 0 |
| TBA-T4W (6eo6) * | 707.6 | 14 | 0 |
| TBA-T4K (6eo7) * | 640.6 | 13 | 0 |
| TBA-3L (6z8v) * | 605.8 | 14 | 0 |
| TBA-3Leu (6z8x) * | 592.2 | 9 | 0 |
| RE31 (5cmx) | 551.7 | 10 | 0 |
| NU172 (6evv) | 589.8 | 10 | 0 |
| Bivalirudin, C-terminal fragment (3vxe) | 566.5 | 6 | 1 |
| Nonapeptide inhibitor (1g37) | 512.0 | 2 | 0 |
| Peptide inhibitor (1eb1) | 544.8 | 4 | 3 |
| Synthetic inhibitor (1ths) * | 534.8 | 6 | 0 |
| Synthetic peptide (2a2x) * | 698.1 | 9 | 0 |
| Exosite I + active site | |||
| Heparin cofactor II (1jmo) | 1743.8 | 30 | 13 |
| Proteinase-activated receptor 1-PAR1 (3lu9) | 1573.5 | 25 | 6 |
| AGAP008004-PA from A. gambiae (5nhu) | 1468.6 | 24 | 8 |
| Anophelin (4e05) | 1425.4 | 29 | 11 |
| Boophilin (2ody) | 1979.4 | 24 | 15 |
| Hirudin variant 1 (2pw8) | 1531.1 | 21 | 6 |
| Hirudin variant 2 (4htc) | 1652.1 | 20 | 15 |
| Ornithodorin (1toc) | 1763.3 | 15 | 7 |
| Rhodniin (1tbr) | 1703.7 | 16 | 10 |
| Variegin (3b23) | 900.0 | 12 | 5 |
| CVS995 synthetic peptide (1dit) | 1159.2 | 18 | 4 |
| Hirulog (1abi) | 1241.6 | 19 | 4 |
| bza-2 hirulog (1qur) * | 1348.3 | 13 | 2 |
| Hirunorm IV (4thn) | 1038.4 | 11 | 11 |
| Hirunorm V (5gds) | 1030.7 | 9 | 5 |
| Hirutonin 2 (1ihs) * | 1334.8 | 16 | 4 |
| Hirutonin 6 (1iht) * | 1027.2 | 14 | 4 |
| Synthetic thrombin inhibitor P798 (1eoj) * | 1188.8 | 8 | 4 |
| Synthetic thrombin inhibitor P596 (1hbt) | 1143.5 | 16 | 0 |
* PDB entries that were manually curated for the analyses.