3t3e: Difference between revisions

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 <StructureSection load='3t3e' size='340' side='right'caption='[[3t3e]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3t3e]] is a 1 chain structure with 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=3T3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3T3E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3t3e]] 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=3T3E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T3E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GPQ:5-CHLORO-1-(BETA-D-GLUCOPYRANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>GPQ</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPQ:5-CHLORO-1-(BETA-D-GLUCOPYRANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE'>GPQ</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3sym|3sym]], [[3syr|3syr]], [[3t3d|3t3d]], [[3t3g|3t3g]], [[3t3h|3t3h]], [[3t3i|3t3i]]</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=3t3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3e OCA], [https://pdbe.org/3t3e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t3e RCSB], [https://www.ebi.ac.uk/pdbsum/3t3e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3e ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3t3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t3e OCA], [http://pdbe.org/3t3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3t3e RCSB], [http://www.ebi.ac.uk/pdbsum/3t3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3t3e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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.
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-C5 halogen substituted glucopyranosyl nucleosides (1-(beta-D-glucopyranosyl)-5-X-uracil; X=Cl, Br, I) have been discovered as some of the most potent active site inhibitors of glycogen phosphorylase (GP), with respective K(i) values of 1.02, 3.27, and 1.94 muM. The ability of the halogen atom to form intermolecular electrostatic interactions through the sigma-hole phenomenon rather than through steric effects alone forms the structural basis of their improved inhibitory potential relative to the unsubstituted 1-(beta-D-glucopyranosyl)uracil (K(i) =12.39 muM), as revealed by X-ray crystallography and modeling calculations exploiting quantum mechanics methods. Good agreement was obtained between kinetics results and relative binding affinities calculated by QM/MM-PBSA methodology for various substitutions at C5. Ex vivo experiments demonstrated that the most potent derivative (X=Cl) toward purified GP has no cytotoxicity and moderate inhibitory potency at the cellular level. In accordance, ADMET property predictions were performed, and suggest decreased polar surface areas as a potential means of improving activity in the cell.
-The sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides towards Glycogen Phosphorylase b.,Kantsadi AL, Hayes JM, Manta S, Skamnaki VT, Kiritsis C, Psarra AM, Koutsogiannis Z, Dimopoulou A, Theofanous S, Nikoleousakos N, Zoumpoulakis P, Kontou M, Papadopoulos G, Zographos SE, Komiotis D, Leonidas DD ChemMedChem. 2012 Jan 20. doi: 10.1002/cmdc.201100533. PMID:22267166<ref>PMID:22267166</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3t3e" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Phosphorylase]]
+[[Category: Kantsadi AL]]
-[[Category: Kantsadi, A L]]
+[[Category: Leonidas DD]]
-[[Category: Leonidas, D D]]
+[[Category: Skamnaki VT]]
-[[Category: Skamnaki, V T]]
-[[Category: A+b protein]]
-[[Category: Muscle]]
-[[Category: Transferase]]
-[[Category: Transferase-transferase inhibitor complex]]