| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | dxh | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712 | 6fni | 95.94 |
| 2 | dwt | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of NVP-BHG712 | 6fnj | 91.18 |
| 3 | x9f | ephB4 kinase domain inhibitor complex | 2x9f | 78.79 |
| 4 | 7x8 | ephB4 kinase domain inhibitor complex | 2vx1 | 77.97 |
| 5 | dxk | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a pyrazolo[3,4-d]pyrimidine fragment of NVP-BHG712 | 6fnk | 77.51 |
| 6 | 7x5 | ephB4 kinase domain inhibitor complex | 2vwy | 76.85 |
| 7 | 7x2 | ephB4 kinase domain inhibitor complex | 2vww | 76.25 |
| 8 | as6 | ephB4 kinase domain inhibitor complex | 2xvd | 75.92 |
| 9 | 7x4 | ephB4 kinase domain inhibitor complex | 2vwx | 75.88 |
| 10 | 7x6 | ephB4 kinase domain inhibitor complex | 2vwz | 74.68 |
| 11 | 7x7 | ephB4 kinase domain inhibitor complex | 2vx0 | 73.84 |
| 12 | 30k | Complex of the EphB4 kinase domain with an oxindole inhibitor | 4aw5 | 71.45 |
| 13 | 1n1 | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with Dasatinib | 6fnm | 71.32 |
| 14 | 32w | ephB4 kinase domain inhibitor complex | 4bb4 | 69.3 |
| 15 | 7x1 | ephB4 kinase domain inhibitor complex | 2vwu | 68.84 |
| 16 | 7x3 | ephB4 kinase domain inhibitor complex | 2vwv | 67.61 |