3k22: Difference between revisions

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 ==Glucocorticoid Receptor with Bound alaninamide 10 with TIF2 peptide==
-<StructureSection load='3k22' size='340' side='right' caption='[[3k22]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3k22' size='340' side='right'caption='[[3k22]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3k22]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K22 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3k22]] is a 4 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=3K22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K22 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JZR:HEXYL+BETA-D-GLUCOPYRANOSIDE'>JZR</scene>, <scene name='pdbligand=JZS:N-[(1R)-2-AMINO-1-METHYL-2-OXOETHYL]-3-(6-METHYL-4-{[3,3,3-TRIFLUORO-2-HYDROXY-2-(TRIFLUOROMETHYL)PROPYL]AMINO}-1H-INDAZOL-1-YL)BENZAMIDE'>JZS</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3k23|3k23]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JZR:HEXYL+BETA-D-GLUCOPYRANOSIDE'>JZR</scene>, <scene name='pdbligand=JZS:N-[(1R)-2-AMINO-1-METHYL-2-OXOETHYL]-3-(6-METHYL-4-{[3,3,3-TRIFLUORO-2-HYDROXY-2-(TRIFLUOROMETHYL)PROPYL]AMINO}-1H-INDAZOL-1-YL)BENZAMIDE'>JZS</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GRL, NR3C1, PGR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3k22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k22 OCA], [https://pdbe.org/3k22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k22 RCSB], [https://www.ebi.ac.uk/pdbsum/3k22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k22 ProSAT]</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=3k22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k22 OCA], [http://pdbe.org/3k22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k22 RCSB], [http://www.ebi.ac.uk/pdbsum/3k22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k22 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/GCR_HUMAN GCR_HUMAN]] Defects in NR3C1 are a cause of glucocorticoid resistance (GCRES) [MIM:[http://omim.org/entry/138040 138040]]; also known as cortisol resistance. It is a hypertensive, hyperandrogenic disorder characterized by increased serum cortisol concentrations. Inheritance is autosomal dominant.<ref>PMID:12050230</ref> <ref>PMID:1704018</ref> <ref>PMID:7683692</ref> <ref>PMID:11589680</ref> <ref>PMID:11701741</ref>
+[https://www.uniprot.org/uniprot/GCR_HUMAN GCR_HUMAN] Defects in NR3C1 are a cause of glucocorticoid resistance (GCRES) [MIM:[https://omim.org/entry/138040 138040]; also known as cortisol resistance. It is a hypertensive, hyperandrogenic disorder characterized by increased serum cortisol concentrations. Inheritance is autosomal dominant.<ref>PMID:12050230</ref> <ref>PMID:1704018</ref> <ref>PMID:7683692</ref> <ref>PMID:11589680</ref> <ref>PMID:11701741</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/GCR_HUMAN GCR_HUMAN]] Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription factor that binds to glucocorticoid response elements (GRE), both for nuclear and mitochondrial DNA, and as a modulator of other transcription factors. Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Could act as a coactivator for STAT5-dependent transcription upon growth hormone (GH) stimulation and could reveal an essential role of hepatic GR in the control of body growth. Involved in chromatin remodeling. Plays a significant role in transactivation.<ref>PMID:21664385</ref>
+[https://www.uniprot.org/uniprot/GCR_HUMAN GCR_HUMAN] Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription factor that binds to glucocorticoid response elements (GRE), both for nuclear and mitochondrial DNA, and as a modulator of other transcription factors. Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Could act as a coactivator for STAT5-dependent transcription upon growth hormone (GH) stimulation and could reveal an essential role of hepatic GR in the control of body growth. Involved in chromatin remodeling. Plays a significant role in transactivation.<ref>PMID:21664385</ref>
 == 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/k2/3k22_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k2/3k22_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 23: / Line 22: @@
 </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=3k22 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Crystallography and computer modeling have been used to exploit a previously unexplored channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole amides showing excellent complementarity to the channel were designed with the assistance of the computational technique AlleGrow. The accuracy of the design process was demonstrated through crystallographic structural determination of the GR ligand-binding domain-agonist complex of the D-prolinamide derivative 11. The utility of the channel was further exemplified through the design of a potent phenylindazole in which structural motifs, seen to interact with the traditional GR ligand pocket, were abandoned and replaced by interactions within the new channel. Occupation of the channel was confirmed with a second GR crystal structure of this truncated D-alaninamide derivative 13. Compound 11 displays properties compatible with development as an intranasal solution formulation, whereas oral bioavailability has been demonstrated with a related truncated exemplar 14. Data with the pyrrolidinone amide 12 demonstrate the potential for further elaboration within the "meta" channel to deliver compounds with selectivity for the desired transrepressive activity of glucocorticoids. The discovery of these interactions with this important receptor offers significant opportunities for the design of novel GR modulators.
-Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor.,Biggadike K, Bledsoe RK, Coe DM, Cooper TW, House D, Iannone MA, Macdonald SJ, Madauss KP, McLay IM, Shipley TJ, Taylor SJ, Tran TB, Uings IJ, Weller V, Williams SP Proc Natl Acad Sci U S A. 2009 Oct 12. PMID:19822747<ref>PMID:19822747</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3k22" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Glucocorticoid receptor|Glucocorticoid receptor]]
+*[[Glucocorticoid receptor 3D structures|Glucocorticoid receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Biggadike, K B]]
+[[Category: Large Structures]]
-[[Category: Bledsoe, R K]]
+[[Category: Biggadike KB]]
-[[Category: Madauss, K P]]
+[[Category: Bledsoe RK]]
-[[Category: McLay, I M]]
+[[Category: Madauss KP]]
-[[Category: Williams, S P]]
+[[Category: McLay IM]]
-[[Category: Alpha helical sandwich]]
+[[Category: Williams SP]]
-[[Category: Alternative initiation]]
-[[Category: Chromatin regulator]]
-[[Category: Disease mutation]]
-[[Category: Dna-binding]]
-[[Category: Glucocorticoid receptor]]
-[[Category: Glucocorticoid]]
-[[Category: Gr]]
-[[Category: Isopeptide bond]]
-[[Category: Lipid-binding]]
-[[Category: Meta-channel]]
-[[Category: Metal-binding]]
-[[Category: Nuclear receptor]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Pseudohermaphroditism]]
-[[Category: Receptor]]
-[[Category: Steroid hormone receptor]]
-[[Category: Steroid-binding]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Zinc-finger]]