3b2r: Difference between revisions

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==Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil==
The line below this paragraph, containing "STRUCTURE_3b2r", creates the "Structure Box" on the page.
<StructureSection load='3b2r' size='340' side='right'caption='[[3b2r]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3b2r]] 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=3B2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B2R FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.07&#8491;</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=VDN:2-{2-ETHOXY-5-[(4-ETHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-5-METHYL-7-PROPYLIMIDAZO[5,1-F][1,2,4]TRIAZIN-4(1H)-ONE'>VDN</scene></td></tr>
{{STRUCTURE_3b2r| PDB=3b2r |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b2r OCA], [https://pdbe.org/3b2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b2r RCSB], [https://www.ebi.ac.uk/pdbsum/3b2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b2r ProSAT]</span></td></tr>
</table>
== Function ==
[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.
== 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/b2/3b2r_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3b2r ConSurf].
<div style="clear:both"></div>


'''Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil'''
==See Also==
 
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Vardenafil has higher affinity to phosphodiesterase-5 (PDE5) than sildenafil and lower administered dosage for the treatment of erectile dysfunction. However, the molecular basis for these differences is puzzling because two drugs have similar chemical structures. Reported here is a crystal structure of the fully active and nonmutated PDE5A1 catalytic domain in complex with vardenafil. The structure shows that the conformation of the H-loop in the PDE5A1-vardenafil complex is different from those of any known structures of the unliganded PDE5 and its complexes with the inhibitors. In addition, the molecular configuration of vardenafil differs from that of sildenafil when bound to PDE5. It is noteworthy that the binding of vardenafil causes loss of the divalent metal ions that have been observed in all the previously published PDE structures. The conformational variation of both PDE5 and the inhibitors provides structural insight into the different potencies of the drugs.
 
==About this Structure==
3B2R is a [[Single protein]] structure of 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=3B2R OCA].
 
==Reference==
Conformational variations of both phosphodiesterase-5 and inhibitors provide the structural basis for the physiological effects of vardenafil and sildenafil., Wang H, Ye M, Robinson H, Francis SH, Ke H, Mol Pharmacol. 2008 Jan;73(1):104-10. Epub 2007 Oct 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17959709 17959709]
[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hengming, K.]]
[[Category: Hengming K]]
[[Category: Howard, R.]]
[[Category: Howard R]]
[[Category: Huanchen, W.]]
[[Category: Huanchen W]]
[[Category: Mengchun, Y.]]
[[Category: Mengchun Y]]
[[Category: Sharron, H F.]]
[[Category: Sharron HF]]
[[Category: Allosteric enzyme]]
[[Category: Alternative splicing]]
[[Category: Cgmp phosphodiesterase]]
[[Category: Cgmp-binding]]
[[Category: Hydrolase]]
[[Category: Levitratm.]]
[[Category: Magnesium]]
[[Category: Metal-binding]]
[[Category: Nucleotide-binding]]
[[Category: Pde5-inhibitor potency]]
[[Category: Phosphorylation]]
[[Category: Polymorphism]]
[[Category: Sildenafil]]
[[Category: Vardenafil]]
[[Category: Zinc]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu May 22 21:48:51 2008''

Latest revision as of 09:26, 21 February 2024

Crystal Structure of PDE5A1 catalytic domain in complex with Vardenafil

3b2r, resolution 2.07Å

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