3ddf: Difference between revisions

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-[[Image:3ddf.png|left|200px]]
-{{STRUCTURE_3ddf|  PDB=3ddf  |  SCENE=  }}
+==GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) pyrrolidin-2-one==
+<StructureSection load='3ddf' size='340' side='right'caption='[[3ddf]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ddf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GB6:(3R,4R,5R)-3,4-DIHYDROXY-5-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDIN-2-ONE'>GB6</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ddf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddf OCA], [https://pdbe.org/3ddf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddf RCSB], [https://www.ebi.ac.uk/pdbsum/3ddf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MAN2_DROME MAN2_DROME] Catalyzes the first committed step in the biosynthesis of complex N-glycans. It controls conversion of high mannose to complex N-glycans; the final hydrolytic step in the N-glycan maturation pathway (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ddf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Refining the chemical structure of functionalized pyrrolidine-based inhibitors of Golgi alpha-mannosidase II (GMII) to optimize binding affinity provided a lead molecule that demonstrated nanomolar competitive inhibition of alpha-mannosidases II and an optimal fit in the active site of Drosophila GMII by X-ray crystallography. Esters of this lead compound also inhibited the growth of human glioblastoma and brain-derived endothelial cells more than the growth of non-tumoral human fibroblasts, suggesting their potential for anti-cancer therapy.
-===GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) pyrrolidin-2-one===
+Functionalized pyrrolidine inhibitors of human type II alpha-mannosidases as anti-cancer agents: optimizing the fit to the active site.,Fiaux H, Kuntz DA, Hoffman D, Janzer RC, Gerber-Lemaire S, Rose DR, Juillerat-Jeanneret L Bioorg Med Chem. 2008 Aug 1;16(15):7337-46. Epub 2008 Jun 14. PMID:18599296<ref>PMID:18599296</ref>
-{{ABSTRACT_PUBMED_18599296}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ddf" style="background-color:#fffaf0;"></div>
-[[3ddf]] is a 1 chain structure of [[Mannosidase]] with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDF OCA].
 ==See Also==
-*[[Mannosidase|Mannosidase]]
+*[[Mannosidase 3D structures|Mannosidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018599296</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
+[[Category: Large Structures]]
-[[Category: Hoffman, D.]]
+[[Category: Hoffman D]]
-[[Category: Kuntz, D A.]]
+[[Category: Kuntz DA]]
-[[Category: Rose, D R.]]
+[[Category: Rose DR]]
-[[Category: Gh38 glycosidase]]
-[[Category: Hydrolase]]