| Index | Ligand Name | Structure | PDB code | Compound Potency nM |
| 1 | as6 | ephB4 kinase domain inhibitor complex | 2xvd | 2 |
| 2 | 7x4 | ephB4 kinase domain inhibitor complex | 2vwx | 40 |
| 3 | x9f | ephB4 kinase domain inhibitor complex | 2x9f | 61 |
| 4 | 7x5 | ephB4 kinase domain inhibitor complex | 2vwy | 90 |
| 5 | 32w | ephB4 kinase domain inhibitor complex | 4bb4 | 190 |
| 6 | 7x8 | ephB4 kinase domain inhibitor complex | 2vx1 | 220 |
| 7 | 7x2 | ephB4 kinase domain inhibitor complex | 2vww | 240 |
| 8 | 7x1 | ephB4 kinase domain inhibitor complex | 2vwu | 350 |
| 9 | 7x7 | ephB4 kinase domain inhibitor complex | 2vx0 | 580 |
| 10 | 30k | Complex of the EphB4 kinase domain with an oxindole inhibitor | 4aw5 | 765 |
| 11 | 7x6 | ephB4 kinase domain inhibitor complex | 2vwz | 794 |
| 12 | 7x3 | ephB4 kinase domain inhibitor complex | 2vwv | 1.6e+004 |