| Index | Ligand Name | Structure | PDB code | ligand desolvation |
| 1 | 738 | Crystal structure of human JNK3 complexed with N-(3-cyano-4,5,6,7-tetrahydro-1-benzothien-2-yl)-2-fluorobenzamide | 2o2u | 92.27 |
| 2 | 880 | THE STRUCTURE OF JNK3 IN COMPLEX WITH AN IMIDAZOLE-PYRIMIDINE INHIBITOR | 4z9l | 89.1 |
| 3 | bz9 | Crystal Structure of human JNK3 complexed with N-(3-methyl-4-(3-(2-(methylamino)pyrimidin-4-yl)pyridin-2-yloxy)naphthalen-1-yl)-1H-benzo[d]imidazol-2-amine | 3da6 | 89.01 |
| 4 | jk3 | JNK3 bound to piperazine amide inhibitor, SR2774. | 3fv8 | 88.78 |
| 5 | snb | Crystal structure of human Jnk3 complexed with a 1-aryl-3,4- dihydroisoquinoline inhibitor | 2waj | 87.81 |
| 6 | kbi | Crystal Structure of JNK3 complexed with CC-930, an orally active anti-fibrotic JNK inhibitor | 3tti | 84.97 |
| 7 | j67 | JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-styrylindolin-2-one | 3g9l | 83.89 |
| 8 | jbi | Crystal Structure of JNK3 complexed with CC-359, a JNK inhibitor for the prevention of ischemia-reperfusion injury | 3ttj | 83.73 |
| 9 | j88 | JNK3 bound to (Z)-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)-4-phenylindolin-2-one | 3g9n | 83.28 |
| 10 | syy | Design and Synthesis of Disubstituted Thiophene and Thiazole Based Inhibitors of JNK for the Treatment of Neurodegenerative Diseases | 3oxi | 82.36 |
| 11 | j72 | JNK-3 bound to (Z)-5-fluoro-1-((6-fluoro-4H-benzo[d][1,3]dioxin-8-yl)methyl)-3-(hydroxyimino)indolin-2-one | 3g90 | 82.1 |
| 12 | 984 | Crystal structure of JNK3 in complex with an imidazole-pyrimidine inhibitor | 1pmn | 81.98 |
| 13 | 3el | Crystal structure of human JNK3 in complex with a benzenesulfonamide inhibitor. | 4u79 | 81.03 |
| 14 | 46c | Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor | 2zdt | 80.66 |
| 15 | 34i | Design and synthesis of brain penetrant selective JNK inhibitors with improved pharmacokinetic properties for the prevention of neurodegeneration | 3rtp | 80.1 |
| 16 | 3h8 | JNK2/3 in complex with 3-(4-{[(2-chlorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide | 4w4v | 79.93 |
| 17 | 3hn | JNK2/3 in complex with 3-(4-{[(4-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(2-methylpyridin-4-yl)benzamide | 4w4x | 79.31 |
| 18 | 932 | Design and Synthesis of a Novel, Orally Efficacious Tri-substituted Thiophene Based JNK Inhibitor | 3ptg | 78.37 |
| 19 | 3wh | The MAP kinase JNK3 as target for halogen bonding | 4x21 | 77.51 |
| 20 | 255 | c-Jun N-terminal Kinase 3 with 3,5-Disubstituted Quinoline inhibitor | 2r9s | 77.45 |
| 21 | jnk | Inhibitor complex of JNK3 | 2exc | 77.04 |
| 22 | 1rq | The crystal structure of inhibitor-bound JNK3 | 4kkh | 76.8 |
| 23 | j07 | Synthesis and SAR of Aminopyrimidines as Novel c-Jun N-Terminal Kinase (JNK) Inhibitors | 2p33 | 76.61 |
| 24 | 0f0 | Discovery of potent and selective covalent inhibitors of JNK | 3v6s | 75.52 |
| 25 | jno | IRAK-4 Inhibitors (Part II)- A structure based assessment of imidazo[1,2 a]pyridine binding | 3cgo | 74.25 |
| 26 | cqq | Discovery of potent and selective covalent inhibitors of JNK | 3v6r | 73.97 |
| 27 | c0m | Crystal structure of human JNK3 complexed with N-{3-cyano-6-[3-(1-piperidinyl)propanoyl]-4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl}-1-naphthalenecarboxamide | 2o0u | 73.35 |
| 28 | 446 | Crystal Structure of human JNK3 complexed with an isoquinolone inhibitor | 2zdu | 73.26 |
| 29 | 3nl | Design and Synthesis of Highly Potent and Isoform Selective JNK3 Inhibitors: SAR Studies on Aminopyrazole Derivatives | 4whz | 71.68 |
| 30 | aiz | inhibitor complex of JNK3 | 2b1p | 68.02 |
| 31 | 4f2 | Pyridopyrimidinone Derivatives as Potent and Selective c-Jun N-Terminal Kinase (JNK) inhibitors | 4y46 | 64.6 |
| 32 | 519 | Pyridopyrimidinone Derivatives as Potent and Selective c-Jun N-Terminal Kinase (JNK) inhibitors | 4y5h | 63.54 |