9RDF
Liver Pyruvate kinase in complex with a phthalazine-based fluorescent probe IV
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Summary for 9RDF
| Entry DOI | 10.2210/pdb9rdf/pdb |
| Group deposition | the group title you wish to show (1) |
| Descriptor | Isoform L-type of Pyruvate kinase PKLR, MAGNESIUM ION, 6-[[7-(dimethylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl]-2-(1~{H}-pyrazol-4-ylmethyl)isoquinolin-1-one, ... (7 entities in total) |
| Functional Keywords | fragment based drug discovery, kinase, hydrolase |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 4 |
| Total formula weight | 237747.21 |
| Authors | Nilssson, O.,Brear, P.,Grotli, M.,Hyvonen, M. (deposition date: 2025-06-02, release date: 2026-04-08) |
| Primary citation | Nilsson, O.,Valaka, A.P.,Haversen, L.,Bogucka, A.,Koteles, I.,Brear, P.,Rutberg, M.,Gunnarsson, A.,Hyvonen, M.,Grotli, M. Potent Fluorescent Probe for Target-Engagement Studies of Allosteric Pyruvate Kinase Modulators. Angew.Chem.Int.Ed.Engl., 64:e202513969-e202513969, 2025 Cited by PubMed Abstract: Pyruvate kinases (PKs) are highly allosterically regulated enzymes that play a central role in cellular metabolism and are increasingly recognized as valuable therapeutic targets in cancer, metabolic diseases, and diabetes. Despite their biological and clinical significance, methods to directly assess allosteric ligand engagement of PK isoforms remain limited. Here, we report the development of LumiPK, a novel, environment-sensitive fluorescent tracer designed to monitor allosteric binding to the liver isoform of pyruvate kinase (PKL). LumiPK integrates an environment-sensitive 4-sulfamonyl-7-aminobenzoxadiazole fluorophore into a potent allosteric modulator scaffold. It emerged as the lead compound from a small ligand series, showing high affinity for PKL (K = 37 ± 5 nM) in recombinant assays; the most potent fluorescent PK reporter reported to date. A NanoBRET assay using a PKL-Nluc fusion (PKL) enabled intracellular monitoring of unlabeled ligand engagement. LumiPK maintained high potency (EC = 18.4 nM) in cellular experiments. Competitive NanoBRET and fluorescence titration assays confirmed binding of known PKL activators (mitapivat, TEPP-46, DASA-58) in both cellular and recombinant settings, with K values remaining consistent across these methods. LumiPK thus provides a robust tool for probing PKL allosteric modulation and fills a key gap in target engagement technologies for PKL. PubMed: 40884041DOI: 10.1002/anie.202513969 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.62 Å) |
Structure validation
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