3dds: Difference between revisions

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-[[Image:3dds.png|left|200px]]
-{{STRUCTURE_3dds|  PDB=3dds  |  SCENE=  }}
+==Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261==
+<StructureSection load='3dds' size='340' side='right'caption='[[3dds]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3dds]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDS 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=26B:O-TERT-BUTYL-N-[(3-{[(2,4,6-TRIMETHYLPHENYL)CARBAMOYL]AMINO}NAPHTHALEN-2-YL)CARBONYL]-L-THREONINE'>26B</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=3dds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dds OCA], [https://pdbe.org/3dds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dds RCSB], [https://www.ebi.ac.uk/pdbsum/3dds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dds ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[https://omim.org/entry/232700 232700]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
+== 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/3dds_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3dds ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.
-===Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK261===
+Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.,Thomson SA, Banker P, Bickett DM, Boucheron JA, Carter HL, Clancy DC, Cooper JP, Dickerson SH, Garrido DM, Nolte RT, Peat AJ, Sheckler LR, Sparks SM, Tavares FX, Wang L, Wang TY, Weiel JE Bioorg Med Chem Lett. 2009 Feb 15;19(4):1177-82. Epub 2008 Dec 25. PMID:19138846<ref>PMID:19138846</ref>
-{{ABSTRACT_PUBMED_19138846}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3dds" style="background-color:#fffaf0;"></div>
-[[3dds]] is a 2 chain structure of [[Glycogen Phosphorylase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDS OCA].
 ==See Also==
-*[[Glycogen Phosphorylase|Glycogen Phosphorylase]]
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019138846</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Phosphorylase]]
+[[Category: Large Structures]]
-[[Category: Nolte, R T.]]
+[[Category: Nolte RT]]
-[[Category: Allosteric enzyme]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Diabetes]]
-[[Category: Disease mutation]]
-[[Category: Glycogen metabolism]]
-[[Category: Glycogen phosphorylase]]
-[[Category: Glycogen storage disease]]
-[[Category: Glycosyltransferase]]
-[[Category: Gp]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transferase]]