2F18

GOLGI ALPHA-MANNOSIDASE II complex with (2R,3R,4S)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol

2F18 の概要

• エントリーDOI: 10.2210/pdb2f18/pdb
• 関連するPDBエントリー: 1HTY 1HWW 1HXK 1PS2 1QWN 1QX1 1R33 1R34 1TQS 1TQT 1TQU 1TQV 1TQW 2ALW 2F1A 2F1B
• 分子名称: Alpha-mannosidase II, 2-acetamido-2-deoxy-beta-D-glucopyranose, PHOSPHATE ION, ... (7 entities in total)
• 機能のキーワード: glycosyl hydrolase family 38, hydrolase
• 由来する生物種: Drosophila melanogaster (fruit fly)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 120453.69

構造登録者

Kuntz, D.A.,Rose, D.R. (登録日: 2005-11-14, 公開日: 2006-12-05, 最終更新日: 2023-08-23)

主引用文献

Englebienne, P.,Fiaux, H.,Kuntz, D.A.,Corbeil, C.R.,Gerber-Lemaire, S.,Rose, D.R.,Moitessier, N.
Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.
Proteins, 69:160-176, 2007

PubMed Abstract: Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.

PubMed: 17557336
DOI: 10.1002/prot.21479

実験手法

X-RAY DIFFRACTION (1.3 Å)