2F1B
GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (2R,3R,4S,5R)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-5-methylpyrrolidine-3,4-diol
Summary for 2F1B
| Entry DOI | 10.2210/pdb2f1b/pdb |
| Related | 1HTY 1HWW 1HXK 1PS2 1QWN 1QX1 1R33 1R34 1TQS 1TQT 1TQU 1TQW 2ALW 2F18 2F1A |
| Descriptor | alpha-mannosidase II, 2-acetamido-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (6 entities in total) |
| Functional Keywords | glycosyl hydrolase family 38, hydrolase |
| Biological source | Drosophila melanogaster (fruit fly) |
| Total number of polymer chains | 1 |
| Total formula weight | 120372.74 |
| Authors | Kuntz, D.A.,Rose, D.R. (deposition date: 2005-11-14, release date: 2006-12-05, Last modification date: 2023-08-23) |
| Primary citation | 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 Cited by 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: 17557336DOI: 10.1002/prot.21479 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.45 Å) |
Structure validation
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