2qrh: Difference between revisions

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-{{Seed}}
-[[Image:2qrh.png|left|200px]]
-<!--
+==Glycogen Phosphorylase b in complex with (1R)-3'-phenylspiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]==
-The line below this paragraph, containing "STRUCTURE_2qrh", creates the "Structure Box" on the page.
+<StructureSection load='2qrh' size='340' side='right'caption='[[2qrh]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2qrh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QRH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QRH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=M08:(5R,7R,8S,9S,10R)-7-(HYDROXYMETHYL)-3-PHENYL-1,6-DIOXA-2-AZASPIRO[4.5]DEC-2-ENE-8,9,10-TRIOL'>M08</scene></td></tr>
-{{STRUCTURE_2qrh|  PDB=2qrh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qrh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qrh OCA], [https://pdbe.org/2qrh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qrh RCSB], [https://www.ebi.ac.uk/pdbsum/2qrh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qrh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT] 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/qr/2qrh_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=2qrh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A series of glucopyranosylidene-spiro-isoxazolines was prepared through regio- and stereoselective [3+2]-cycloaddition between the methylene acetylated exo-glucal and aromatic nitrile oxides. The deprotected cycloadducts were evaluated as inhibitors of muscle glycogen phosphorylase b. The carbohydrate-based family of five inhibitors displays K(i) values ranging from 0.63 to 92.5 microM. The X-ray structures of the enzyme-ligand complexes show that the inhibitors bind preferentially at the catalytic site of the enzyme retaining the less active T-state conformation. Docking calculations with GLIDE in extra-precision (XP) mode yielded excellent agreement with experiment, as judged by comparison of the predicted binding modes of the five ligands with the crystallographic conformations and the good correlation between the docking scores and the experimental free binding energies. Use of docking constraints on the well-defined positions of the glucopyranose moiety in the catalytic site and redocking of GLIDE-XP poses using electrostatic potential fit-determined ligand partial charges in quantum polarized ligand docking (QPLD) produced the best results in this regard.
-===Glycogen Phosphorylase b in complex with (1R)-3'-phenylspiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]===
+Glucose-based spiro-isoxazolines: a new family of potent glycogen phosphorylase inhibitors.,Benltifa M, Hayes JM, Vidal S, Gueyrard D, Goekjian PG, Praly JP, Kizilis G, Tiraidis C, Alexacou KM, Chrysina ED, Zographos SE, Leonidas DD, Archontis G, Oikonomakos NG Bioorg Med Chem. 2009 Oct 15;17(20):7368-80. Epub 2009 Sep 2. PMID:19781947<ref>PMID:19781947</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qrh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19781947}}, adds the Publication Abstract to the page
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19781947 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19781947}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-QRH is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QRH OCA].
-==Reference==
-<ref group="xtra">PMID:19781947</ref><references group="xtra"/>
 [[Category: Oryctolagus cuniculus]]
-[[Category: Phosphorylase]]
+[[Category: Alexacou K-M]]
-[[Category: Alexacou, K M.]]
+[[Category: Chrysina ED]]
-[[Category: Chrysina, E D.]]
+[[Category: Kizilis G]]
-[[Category: Kizilis, G.]]
+[[Category: Leonidas DD]]
-[[Category: Leonidas, D D.]]
+[[Category: Oikonomakos NG]]
-[[Category: Oikonomakos, N G.]]
+[[Category: Zographos SE]]
-[[Category: Zographos, S E.]]
-[[Category: Acetylation]]
-[[Category: Allosteric enzyme]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Glycogen metabolism]]
-[[Category: Glycogenolysis]]
-[[Category: Glycosyltransferase]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphorylation]]
-[[Category: Pyridoxal phosphate]]
-[[Category: Transferase]]
-[[Category: Type 2 diabetes]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 11 22:44:45 2009''