6YKD
Human Pim-1 kinase in complex with an inhibitor identified by virtual screening
Summary for 6YKD
| Entry DOI | 10.2210/pdb6ykd/pdb |
| Descriptor | Serine/threonine-protein kinase pim-1, ~{N}-[3-[6-[(3~{R})-piperidin-3-yl]-2-pyridin-4-yl-pyrimidin-4-yl]oxyphenyl]ethanamide, GLYCEROL, ... (5 entities in total) |
| Functional Keywords | kinase, cancer, transferase, atp-binding, virtual screening, apoptosis |
| Biological source | Homo sapiens (Human) |
| Total number of polymer chains | 1 |
| Total formula weight | 38265.27 |
| Authors | Schneider, P.,Welin, M.,Svensson, B.,Walse, B.,Schneider, G. (deposition date: 2020-04-06, release date: 2020-07-01, Last modification date: 2024-11-06) |
| Primary citation | Schneider, P.,Welin, M.,Svensson, B.,Walse, B.,Schneider, G. Virtual Screening and Design with Machine Intelligence Applied to Pim-1 Kinase Inhibitors. Mol Inform, 39:e2000109-e2000109, 2020 Cited by PubMed Abstract: Ligand-based virtual screening of large compound collections, combined with fast bioactivity determination, facilitate the discovery of bioactive molecules with desired properties. Here, chemical similarity based machine learning and label-free differential scanning fluorimetry were used to rapidly identify new ligands of the anticancer target Pim-1 kinase. The three-dimensional crystal structure complex of human Pim-1 with ligand bound revealed an ATP-competitive binding mode. Generative de novo design with a recurrent neural network additionally suggested innovative molecular scaffolds. Results corroborate the validity of the chemical similarity principle for rapid ligand prototyping, suggesting the complementarity of similarity-based and generative computational approaches. PubMed: 33448694DOI: 10.1002/minf.202000109 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.86 Å) |
Structure validation
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