3shy

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Current revision (08:36, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3shy' size='340' side='right'caption='[[3shy]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
<StructureSection load='3shy' size='340' side='right'caption='[[3shy]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3shy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SHY FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3shy]] is a 1 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=3SHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SHY FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FO:6-ETHYL-5-FLUORO-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE'>5FO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.647&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1t9r|1t9r]], [[3shz|3shz]], [[3sie|3sie]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FO:6-ETHYL-5-FLUORO-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE'>5FO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDE5, PDE5A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3',5'-cyclic-GMP_phosphodiesterase 3',5'-cyclic-GMP phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.35 3.1.4.35] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3shy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3shy OCA], [https://pdbe.org/3shy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3shy RCSB], [https://www.ebi.ac.uk/pdbsum/3shy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3shy 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=3shy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3shy OCA], [https://pdbe.org/3shy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3shy RCSB], [https://www.ebi.ac.uk/pdbsum/3shy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3shy ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/PDE5A_HUMAN PDE5A_HUMAN]] Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'-GMP.
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[https://www.uniprot.org/uniprot/PDE5A_HUMAN PDE5A_HUMAN] Plays a role in signal transduction by regulating the intracellular concentration of cyclic nucleotides. This phosphodiesterase catalyzes the specific hydrolysis of cGMP to 5'-GMP.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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For proof-of-concept of halogen bonding in drug design, a series of halogenated compounds were designed based on a lead structure as new inhibitors of phosphodiesterase type 5. Bioassay results revealed a good correlation between the measured bioactivity and the calculated halogen bond energy. Our X-ray crystal structures verified the existence of the predicted halogen bonds, demonstrating that the halogen bond is an applicable tool in drug design and should be routinely considered in lead optimization.
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Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors.,Xu Z, Liu Z, Chen T, Chen T, Wang Z, Tian G, Shi J, Wang X, Lu Y, Yan X, Wang G, Jiang H, Chen K, Wang S, Xu Y, Shen J, Zhu W J Med Chem. 2011 Aug 11;54(15):5607-11. Epub 2011 Jul 14. PMID:21714539<ref>PMID:21714539</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3shy" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
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[[Category: Homo sapiens]]
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[[Category: Human]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Chen, T]]
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[[Category: Chen T]]
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[[Category: Chen, T T]]
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[[Category: Chen TT]]
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[[Category: Xu, Y C]]
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[[Category: Xu YC]]
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[[Category: Hydrolase-hydrolase inhibitor complex]]
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[[Category: Pde5a inhibitor]]
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Current revision

Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

PDB ID 3shy

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