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==Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors==
==Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors==
<StructureSection load='4oew' size='340' side='right' caption='[[4oew]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
<StructureSection load='4oew' size='340' side='right'caption='[[4oew]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4oew]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tsf 3tsf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OEW FirstGlance]. <br>
<table><tr><td colspan='2'>[[4oew]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tsf 3tsf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OEW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OEW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5IO:6-ETHYL-5-IODO-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE'>5IO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.44&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4oex|4oex]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IO:6-ETHYL-5-IODO-2-{5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-2-PROPOXYPHENYL}PYRIMIDIN-4(3H)-ONE'>5IO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3',5'-cyclic-GMP_phosphodiesterase 3',5'-cyclic-GMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.35 3.1.4.35] </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=4oew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oew OCA], [https://pdbe.org/4oew PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4oew RCSB], [https://www.ebi.ac.uk/pdbsum/4oew PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4oew 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=4oew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oew OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oew RCSB], [http://www.ebi.ac.uk/pdbsum/4oew PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.
 
Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors.,Ren J, He Y, Chen W, Chen T, Wang G, Wang Z, Xu Z, Luo X, Zhu W, Jiang H, Shen J, Xu Y J Med Chem. 2014 Apr 24;57(8):3588-93. doi: 10.1021/jm5002315. Epub 2014 Apr 15. PMID:24702184<ref>PMID:24702184</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
[[Category: Homo sapiens]]
[[Category: Chen, T T]]
[[Category: Large Structures]]
[[Category: Ren, J]]
[[Category: Chen TT]]
[[Category: Xu, Y C]]
[[Category: Ren J]]
[[Category: Hydrolase]]
[[Category: Xu YC]]
[[Category: Hydrolase-hydrolase inhibitor complex]]

Latest revision as of 12:39, 1 March 2024

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

4oew, resolution 2.44Å

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