| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | mi1 | Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6 | 3lxk | 95.16 |
| 2 | g54 | JAK3 with Cyanamide CP23 | 6db3 | 92.01 |
| 3 | 79s | Crystal structure of JAK3 in complex with Compound 5 (FM409) | 5lwn | 90.74 |
| 4 | 7kv | Jak3 with covalent inhibitor 7 | 5ttu | 90.33 |
| 5 | gyw | HUMAN JAK3 IN COMPLEX WITH LASW959 PROTEIN IN COMPLEX WITH LIGAND | 6hzv | 89.26 |
| 6 | 19s | JAK3 kinase domain in complex with 2-Cyclopropyl-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((R)-1-methyl-2-oxo-2-piperidin-1-yl-ethyl)-amide | 4hvi | 89.02 |
| 7 | g4y | JAK3 with Cyanamide CP34 | 6db4 | 88.68 |
| 8 | vfc | Crystal structure of JAK3 kinase domain in complex with an indazole substituted pyrrolopyrazine inhibitor | 3zc6 | 88.2 |
| 9 | 79r | Crystal structure of JAK3 in complex with Compound 5 (FM409) | 5lwn | 88.07 |
| 10 | hb4 | JAK3 with cyanamide CP12 | 6dud | 87.51 |
| 11 | 3qx | Crystal structure of JAK3 kinase domain in complex with a pyrrolopyridazine carboxamide inhibitor | 4rio | 86.93 |
| 12 | 19q | JAK3 kinase domain in complex with 2-Cyclopropyl-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((S)-2-hydroxy-1,2-dimethyl-propyl)-amide | 4hvg | 86.69 |
| 13 | 3c9 | JAK3 kinase domain in complex with 1-[(3S)-1-isobutylsulfonyl-3-piperidyl]-3-(5H-pyrrolo[2,3-b]pyrazin-2-yl)urea | 4qt1 | 86.66 |
| 14 | 19r | JAK3 kinase domain in complex with 2-Cyclopropyl-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((R)-2-hydroxy-1,2-dimethyl-propyl | 4hvh | 86.26 |
| 15 | 9z4 | THE JAK3 KINASE DOMAIN IN COMPLEX WITH A COVALENT INHIBITOR | 5wfj | 85.6 |
| 16 | 933 | JAK3 kinase domain in complex with 2-Cyclopropyl-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((S)-1,2,2-trimethyl-propyl)-amide | 4hvd | 85.58 |
| 17 | f3w | Crystal structure of JAK3 in complex with Compound 10 (FM475) | 6gl9 | 85.51 |
| 18 | f48 | Crystal structure of JAK3 in complex with Compound 20 (FM484) | 6glb | 84.68 |
| 19 | g4v | JAK3 with Cyanamide CP10 | 6da4 | 83.75 |
| 20 | 1dt | JAK3 kinase domain in complex with 2-Phenoxy-5H-pyrrolo[2,3-b]pyrazine-7-carboxylic acid ((S)-1-cyclopropyl-ethyl)-amide | 4i6q | 83.4 |
| 21 | 9t6 | Crystal structure of JAK3 in complex with peficitinib | 6aak | 81.99 |
| 22 | 7kx | Jak3 with covalent inhibitor 6 | 5ttv | 81.5 |
| 23 | 7h4 | JAK3 with covalent inhibitor PF-06651600 | 5toz | 81.35 |
| 24 | 9j4 | CRYSTAL STRUCTURE OF JAK3 KINASE DOMAIN IN COMPLEX WITH A PYRROLOPYRIDAZINE INHIBITOR | 5vo6 | 81.19 |
| 25 | z3a | Crystal structure of JAK3 kinase domain in complex with a pyrrolopyridazine carboxamide inhibitor | 6ny4 | 80.73 |
| 26 | 7ku | Jak3 with covalent inhibitor 4 | 5tts | 80.63 |
| 27 | 79t | Crystal structure of JAK3 in complex with Compound 4 (FM381) | 5lwm | 76.26 |
| 28 | 1nx | Crystal Structure of JAK3 Kinase Domain in Complex with a Pyrrolopyrazine-2-phenyl Ether Inhibitor | 3zep | 75.19 |
| 29 | g9b | JAK3 in complex with a covalent EGFR inhibitor | 4v0g | 73.06 |
| 30 | 4lh | Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N-(3-(((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)pyrimidin-4-yl)amino)methyl)phenyl)acrylamide | 4z16 | 72.01 |
| 31 | 9yv | CRYSTAL STRUCTURE OF JAK3 KINASE DOMAIN WITH A 4,6-DIAMINONICOTINAMIDE INHIBITOR (COMPOUND NUMBER 7) | 5w86 | 69.22 |