4MMM

Human Pdrx5 complex with a ligand BP7

4MMM の概要

• エントリーDOI: 10.2210/pdb4mmm/pdb
• 関連するPDBエントリー: 4K7I 4K7N 4K7O
• 分子名称: Peroxiredoxin-5, mitochondrial, 1,1'-BIPHENYL-3,4-DIOL (3 entities in total)
• 機能のキーワード: enzyme, oxidoreductase
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Isoform Mitochondrial: Mitochondrion. Isoform Cytoplasmic+peroxisomal: Cytoplasm: P30044
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 71714.31

構造登録者

Guichou, J.F. (登録日: 2013-09-09, 公開日: 2014-07-30, 最終更新日: 2024-03-20)

主引用文献

Aguirre, C.,Brink, T.T.,Guichou, J.F.,Cala, O.,Krimm, I.
Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5
Plos One, 9:e102300-e102300, 2014

PubMed Abstract: Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.

PubMed: 25025339
DOI: 10.1371/journal.pone.0102300

実験手法

X-RAY DIFFRACTION (1.47 Å)