3k3h: Difference between revisions

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-[[Image:3k3h.png|left|200px]]
-{{STRUCTURE_3k3h|  PDB=3k3h  |  SCENE=  }}
+==Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691==
+<StructureSection load='3k3h' size='340' side='right'caption='[[3k3h]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3k3h]] 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=3K3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K3H 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BYE:1-(2-CHLOROPHENYL)-6-[(2S)-3,3,3-TRIFLUORO-2-METHYLPROPYL]-1,7-DIHYDRO-4H-PYRAZOLO[3,4-D]PYRIMIDIN-4-ONE'>BYE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3k3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k3h OCA], [https://pdbe.org/3k3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k3h RCSB], [https://www.ebi.ac.uk/pdbsum/3k3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k3h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDE9A_HUMAN PDE9A_HUMAN] Hydrolyzes the second messenger cGMP, which is a key regulator of many important physiological processes.<ref>PMID:18757755</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/k3/3k3h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3k3h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+PDE9 inhibitors have been studied as therapeutics for treatment of cardiovascular diseases, diabetes, and neurodegenerative disorders. To illustrate the inhibitor selectivity, the crystal structures of the PDE9A catalytic domain in complex with the enantiomers of PDE9 inhibitor 1-(2-chlorophenyl)-6-(3,3,3-trifluoro-2-methylpropyl)-1H-pyrazolo[3,4-d]py rimidine-4(5H)-one ((R)-BAY73-6691 or (S)-BAY73-6691, 1r or 1s) were determined and mutagenesis was performed. The structures showed that the fluoromethyl groups of 1r and 1s had different orientations while the other parts of the inhibitors commonly interacted with PDE9A. These differences may explain the slightly different affinity of 1r (IC(50) = 22 nM) and 1s (IC(50) = 88 nM). The mutagenesis experiments revealed that contribution of the binding residues to the inhibitor sensitivity varies dramatically, from few-fold to 3 orders of magnitude. On the basis of the crystal structures, a hypothesized compound that simulates the recently published PDE9 inhibitors was modeled to provide insight into the inhibitor selectivity.
-===Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691===
+Insight into Binding of Phosphodiesterase-9A Selective Inhibitors by Crystal Structures and Mutagenesis.,Wang H, Luo X, Ye M, Hou J, Robinson H, Ke H J Med Chem. 2010 Feb 1. PMID:20121115<ref>PMID:20121115</ref>
-{{ABSTRACT_PUBMED_20121115}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3k3h" style="background-color:#fffaf0;"></div>
-[[3k3h]] is a 2 chain structure of [[Phosphodiesterase]] 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=3K3H OCA].
 ==See Also==
-*[[Phosphodiesterase|Phosphodiesterase]]
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020121115</ref><references group="xtra"/>
+__TOC__
-[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Hou, J.]]
+[[Category: Large Structures]]
-[[Category: Ke, H.]]
+[[Category: Hou J]]
-[[Category: Luo, X.]]
+[[Category: Ke H]]
-[[Category: Robinson, H.]]
+[[Category: Luo X]]
-[[Category: Wang, H.]]
+[[Category: Robinson H]]
-[[Category: Ye, M.]]
+[[Category: Wang H]]
-[[Category: Catalytic domain]]
+[[Category: Ye M]]
-[[Category: Cgmp]]
-[[Category: Hydrolase]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Pde9]]
-[[Category: Phosphoprotein]]