2F1A: Golgi Alpha-Mannosidase Ii Complex With (2r,3r,4s)-2-({[(1s)-2- Hydroxy-1-Phenylethyl]amino}methyl)pyrrolidine-3,4-Diol

Citation:
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.
PDB ID: 2F1ADownload
MMDB ID: 42722
PDB Deposition Date: 2005/11/14
Updated in MMDB: 2006/12
Experimental Method:
x-ray diffraction
Resolution: 1.45  Å
Source Organism:
Similar Structures:
Biological Unit for 2F1A: monomeric; determined by author
Molecular Components in 2F1A
Label Count Molecule
Protein (1 molecule)
1
Alpha-mannosidase II
Molecule annotation
Chemicals (5 molecules)
1
1
2
1
3
1
4
1
5
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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