6zdr: Difference between revisions
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<StructureSection load='6zdr' size='340' side='right'caption='[[6zdr]], [[Resolution|resolution]] 1.92Å' scene=''> | <StructureSection load='6zdr' size='340' side='right'caption='[[6zdr]], [[Resolution|resolution]] 1.92Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'> | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZDR 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]] 1.918Å</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]] 1.918Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=QGE:[3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl]+ethanoate'>QGE</scene></td></tr> | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=QGE:[3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl]+ethanoate'>QGE</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=6zdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zdr OCA], [https://pdbe.org/6zdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zdr RCSB], [https://www.ebi.ac.uk/pdbsum/6zdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zdr ProSAT]</span></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=6zdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zdr OCA], [https://pdbe.org/6zdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zdr RCSB], [https://www.ebi.ac.uk/pdbsum/6zdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zdr ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Aqvist J]] | [[Category: Aqvist J]] | ||
Latest revision as of 16:21, 6 November 2024
Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4dCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4d
Structural highlights
Publication Abstract from PubMedWe present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2A AR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2A AR, an emerging target in immuno-oncology. X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists.,Jespers W, Verdon G, Azuaje J, Majellaro M, Keranen H, Garcia-Mera X, Congreve M, Deflorian F, de Graaf C, Zhukov A, Dore AS, Mason JS, Aqvist J, Cooke RM, Sotelo E, Gutierrez-de-Teran H Angew Chem Int Ed Engl. 2020 Jun 16. doi: 10.1002/anie.202003788. PMID:32542862[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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