4ia0 - Revision history

OCA at 08:51, 9 November 2022

2022-11-09T08:51:03Z

←Older revision		Revision as of 08:51, 9 November 2022
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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='4ia0' size='340' side='right' caption='[[4ia0]], [[Resolution\|resolution]] 2.17Å' scene=''>	+	<StructureSection load='4ia0' size='340' side='right'caption='[[4ia0]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ia0]] is a 1 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=4IA0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4IA0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ia0]] 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=4IA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IA0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BB:5-BROMO-2-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-6-OCTYLPYRIMIDIN-4(3H)-ONE'>5BB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BB:5-BROMO-2-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-6-OCTYLPYRIMIDIN-4(3H)-ONE'>5BB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i9z\|4i9z]]</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=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [https://pdbe.org/4ia0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ia0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ia0 ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE5, PDE5A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [~~http~~://pdbe.org/4ia0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ia0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ia0 ProSAT]</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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3',5'-cyclic-GMP phosphodiesterase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Chen, T]]	+	[[Category: Chen T]]
-	[[Category: Ren, J]]	+	[[Category: Ren J]]
-	[[Category: Xu, Y]]	+	[[Category: Xu Y]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 10:42, 4 August 2016

2016-08-04T10:42:06Z

←Older revision		Revision as of 10:42, 4 August 2016
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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='4ia0' size='340' side='right' caption='[[4ia0]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='4ia0' size='340' side='right' caption='[[4ia0]], [[Resolution\|resolution]] 2.17Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE5, PDE5A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE5, PDE5A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ia0 PDBsum]</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=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [http://pdbe.org/4ia0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ia0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ia0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4ia0" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:27, 25 December 2014

2014-12-25T08:27:54Z

←Older revision		Revision as of 08:27, 25 December 2014
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	<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=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ia0 PDBsum]</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=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ia0 PDBsum]</span></td></tr>
	</table>		</table>
		+	== 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:28, 21 December 2014

2014-12-21T17:28:45Z

←Older revision		Revision as of 17:28, 21 December 2014
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-	~~{{STRUCTURE_4ia0\| PDB=4ia0 \| SCENE= }}~~	+	==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='4ia0' size='340' side='right' caption='[[4ia0]], [[Resolution\|resolution]] 2.17Å' scene=''>
-	{~~{ABSTRACT_PUBMED_23867165}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ia0]] is a 1 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=4IA0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IA0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BB:5-BROMO-2-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-6-OCTYLPYRIMIDIN-4(3H)-ONE'>5BB</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4i9z\|4i9z]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE5, PDE5A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ia0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ia0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ia0 RCSB], [http://www.ebi.ac.uk/pdbsum/4ia0 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The substituents both at the 6-position of the 5-bromopyrimidinone ring and at the 5'-position of the phenyl ring of 5-bromopyrimidin-4(3H)-ones were explored. 5-Bromo-6-isopropyl-2-(2-propoxy-phenyl)pyrimidin-4(3H)-one was identified as a new scaffold for potent PDE5 inhibitors. The crystal structures of PDE5/2e and PDE5/10a complexes provided a structural basis for the inhibition of 5-bromopyrimidinones to PDE5. In addition, it was also found that there is a great tolerance for the substitution at the 5'-position of the phenyl ring of 5-bormopyrimidinones and the resulted compound 13a has the highest inhibition activity to PDE5 (IC50, 1.7 nM).

-	~~==Function==~~	+	Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5.,Gong X, Wang G, Ren J, Liu Z, Wang Z, Chen T, Yang X, Jiang X, Shen J, Jiang H, Aisa HA, Xu Y, Li J Bioorg Med Chem Lett. 2013 Sep 1;23(17):4944-7. doi: 10.1016/j.bmcl.2013.06.062. , Epub 2013 Jun 29. PMID:23867165<ref>PMID:23867165</ref>
-	~~[[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~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4ia0]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4IA0 OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:023867165</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Phosphodiesterase\|Phosphodiesterase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: 3',5'-cyclic-GMP phosphodiesterase]]		[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
-	[[Category: Chen, T.]]	+	[[Category: Human]]
-	[[Category: Ren, J.]]	+	[[Category: Chen, T]]
-	[[Category: Xu, Y.]]	+	[[Category: Ren, J]]
		+	[[Category: Xu, Y]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 12:08, 1 January 2014

2014-01-01T12:08:32Z

←Older revision		Revision as of 12:08, 1 January 2014
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4ia0\| PDB=4ia0 \| SCENE= }}
		+	===Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors===
		+	{{ABSTRACT_PUBMED_23867165}}

-	~~The entry 4ia0 is ON HOLD until Paper Publication~~	+	==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.

-	~~Authors: Ren, J~~.~~, Chen, T~~.T.~~, Xu, Y~~.C.	+	==About this Structure==
		+	[[4ia0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IA0 OCA].

-	~~Description~~: ~~Crystal structure of the PDE5A1 catalytic domain in~~ complex ~~with novel inhibitors~~	+	==Reference==
		+	<ref group="xtra">PMID:023867165</ref><references group="xtra"/><references/>
		+	[[Category: 3',5'-cyclic-GMP phosphodiesterase]]
		+	[[Category: Chen, T.]]
		+	[[Category: Ren, J.]]
		+	[[Category: Xu, Y.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 16:12, 20 March 2013

2013-03-20T16:12:39Z

←Older revision		Revision as of 16:12, 20 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ia0 is ON HOLD	+	The entry 4ia0 is ON HOLD until Paper Publication

	Authors: Ren, J., Chen, T.T., Xu, Y.C.		Authors: Ren, J., Chen, T.T., Xu, Y.C.

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

OCA at 11:05, 19 December 2012

2012-12-19T11:05:11Z

←Older revision		Revision as of 11:05, 19 December 2012
Line 3:		Line 3:
	The entry 4ia0 is ON HOLD		The entry 4ia0 is ON HOLD

-	Authors: Ren,J., Chen,T.T., Xu,Y.C.	+	Authors: Ren, J., Chen, T.T., Xu, Y.C.

-	Description: ~~CRYSTAL STRUCTURE OF THE~~ PDE5A1 ~~CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS~~	+	Description: Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

OCA: Protected "4ia0" [edit=sysop:move=sysop]

2012-12-12T20:52:12Z

Protected "4ia0" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:52, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 4ia0 is ON HOLD Authors: Ren,J., Chen,T.T., Xu,Y.C. Description: CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS

2012-12-12T20:52:11Z

New page: '''Unreleased structure''' The entry 4ia0 is ON HOLD Authors: Ren,J., Chen,T.T., Xu,Y.C. Description: CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS

New page

'''Unreleased structure'''

The entry 4ia0 is ON HOLD

Authors: Ren,J., Chen,T.T., Xu,Y.C.

Description: CRYSTAL STRUCTURE OF THE PDE5A1 CATALYTIC DOMAIN IN COMPLEX WITH NOVEL INHIBITORS