Summary for 9GBJ
| Entry DOI | 10.2210/pdb9gbj/pdb |
| Descriptor | GTPase KRas, GUANOSINE-5'-DIPHOSPHATE, 1-[(3S)-1-[2-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]-6-[(1S)-1-[(2S)-1-methylpyrrolidin-2-yl]ethoxy]pyrimidin-4-yl]pyrrolidin-3-yl]-3-[1-(methoxymethyl)cyclopropyl]urea, ... (5 entities in total) |
| Functional Keywords | covalent inhibitor, irreversible inhibitor, aspartic acid, kras, carbodiimide, hydrolase |
| Biological source | Homo sapiens (human) |
| Total number of polymer chains | 1 |
| Total formula weight | 20515.12 |
| Authors | Sirocchi, L.S.,Zak, K.M.,Wilding, B. (deposition date: 2024-07-31, release date: 2025-04-30, Last modification date: 2025-05-21) |
| Primary citation | Sirocchi, L.S.,Scharnweber, M.,Oberndorfer, S.,Siszler, G.,Zak, K.M.,Rumpel, K.,Neumuller, R.A.,Wilding, B. Discovery of Carbodiimide Warheads to Selectively and Covalently Target Aspartic Acid in KRAS G12D . J.Am.Chem.Soc., 147:15787-15795, 2025 Cited by PubMed Abstract: Targeted covalent inhibitors are known to be successful therapeutics used in various indications. Covalent drugs typically target cysteine, as cysteine is well suited due to its high nucleophilicity. However, its low abundance in protein binding sites represents a major limitation. As a result, there is a need to covalently target additional nucleophilic amino acids. Recent literature has reported covalent inhibitors labeling aspartic acid in KRAS. However, these compounds also covalently bind to KRAS, indicating their cross-reactivity to cysteine along with aspartic acid. We report here carbodiimides as a novel reactive group to selectively target aspartic acid. Covalent inhibitors bearing a carbodiimide moiety are shown to covalently label KRAS in biochemical and cellular assays. A high-resolution X-ray crystal structure was obtained, which illustrates the mechanism of the covalent bond formation with KRAS. Carbodiimide warheads show selectivity toward KRAS over other KRAS alleles and represent a new covalent warhead suitable for covalently binding to aspartic acid in a biochemical and cellular context. PubMed: 40267480DOI: 10.1021/jacs.5c03562 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.712 Å) |
Structure validation
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