3NK8

Trypsin in complex with fluorine-containing fragment

3NK8 の概要

• エントリーDOI: 10.2210/pdb3nk8/pdb
• 関連するPDBエントリー: 3NKK
• 分子名称: Cationic trypsin, DIMETHYL SULFOXIDE, CALCIUM ION, ... (5 entities in total)
• 機能のキーワード: beta barrel, chymotrypsin double beta barrel, peptide hydrolase, calcium binding, pancreas-duodenum, hydrolase
• 由来する生物種: Bos taurus (Bovine)
• 細胞内の位置: Secreted, extracellular space: P00760
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 23880.06

構造登録者

Schiering, N.,Vulpetti, A.,Dalvit, C. (登録日: 2010-06-18, 公開日: 2010-11-10, 最終更新日: 2024-11-20)

主引用文献

Vulpetti, A.,Schiering, N.,Dalvit, C.
Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments.
Proteins, 78:3281-3291, 2010

PubMed Abstract: (19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description.

PubMed: 20886466
DOI: 10.1002/prot.22836

実験手法

X-RAY DIFFRACTION (1.15 Å)