8QE7

NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 2-(methylsulfonylmethyl)-1H-benzimidazole

8QE7 の概要

• エントリーDOI: 10.2210/pdb8qe7/pdb
• 関連するPDBエントリー: 8QDK
• NMR情報: BMRB: 34860
• 分子名称: RASK GTPase (Fragment), 2-[(methylsulfonyl)methyl]-1H-benzimidazole (2 entities in total)
• 機能のキーワード: complex, fragment, oncoprotein
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 19508.03

構造登録者

Buetikofer, M.,Orts, J. (登録日: 2023-08-30, 公開日: 2024-09-11, 最終更新日: 2025-05-07)

主引用文献

Butikofer, M.,Torres, F.,Kadavath, H.,Gamperli, N.,Abi Saad, M.J.,Zindel, D.,Coudevylle, N.,Riek, R.,Orts, J.
NMR2-Based Drug Discovery Pipeline Presented on the Oncogenic Protein KRAS.
J.Am.Chem.Soc., 147:13200-13209, 2025

PubMed Abstract: Fragment-based drug discovery has emerged as a powerful approach for developing therapeutics against challenging targets, including the GTPase KRAS. Here, we report an NMR-based screening campaign employing state-of-the-art techniques to evaluate a library of 890 fragments against the oncogenic KRAS G12V mutant bound to GMP-PNP. Further HSQC titration experiments identified hits with low millimolar affinities binding within the SI/SII switch region, which forms the binding interface for the effector proteins. To elucidate the binding modes, we applied NMR molecular replacement (MR) structure calculations, bypassing the need for a conventional protein resonance assignment. Traditionally, MR relies on isotope-filtered nuclear Overhauser effect spectroscopy experiments requiring double-labeled [C,N]-protein. We introduce a cost-efficient alternative using a relaxation-based filter that eliminates isotope labeling while preserving structural accuracy. Validation against standard isotopically labeled workflows confirmed the equivalence of the derived protein-ligand structures. This approach enabled the determination of 12 MR KRAS-fragment complex structures, providing critical insights into structure-activity relationships to guide ligand optimization. These results demonstrate the streamlined integration of MR into a fragment-based drug discovery pipeline composed of screening, binding characterization, and rapid structural elucidation with or without isotopic labeling.

PubMed: 40228104
DOI: 10.1021/jacs.4c16762

実験手法

SOLUTION NMR