OCA at 13:18, 1 February 2024

OCA — Thu, 01 Feb 2024 13:18:44 GMT

←Older revision		Revision as of 13:18, 1 February 2024
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	==Crystal structure of PDE6D in complex with Compound-2==		==Crystal structure of PDE6D in complex with Compound-2==
-	<StructureSection load='7qjk' size='340' side='right'caption='[[7qjk]]' scene=''>	+	<StructureSection load='7qjk' size='340' side='right'caption='[[7qjk]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7qjk]] is a 4 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=7QJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QJK FirstGlance]. <br>
-	</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=7qjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qjk OCA], [https://pdbe.org/7qjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qjk RCSB], [https://www.ebi.ac.uk/pdbsum/7qjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qjk ProSAT]</span></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]] 3.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9VO:N-(phenylmethyl)pyridin-2-amine'>9VO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7qjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qjk OCA], [https://pdbe.org/7qjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qjk RCSB], [https://www.ebi.ac.uk/pdbsum/7qjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qjk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PDE6D_HUMAN PDE6D_HUMAN] Acts as a GTP specific dissociation inhibitor (GDI). Increases the affinity of ARL3 for GTP by several orders of magnitude and does so by decreasing the nucleotide dissociation rate. Stabilizes Arl3-GTP by decreasing the nucleotide dissociation (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RAS is a major anticancer drug target which requires membrane localization to activate downstream signal transduction. The direct inhibition of RAS has proven to be challenging. Here, we present a novel strategy for targeting RAS by stabilizing its interaction with the prenyl-binding protein PDE6D and disrupting its localization. Using rationally designed RAS point mutations, we were able to stabilize the RAS:PDE6D complex by increasing the affinity of RAS for PDE6D, which resulted in the redirection of RAS to the cytoplasm and the primary cilium and inhibition of oncogenic RAS/ERK signaling. We developed an SPR fragment screening and identified fragments that bind at the KRAS:PDE6D interface, as shown through cocrystal structures. Finally, we show that the stoichiometric ratios of KRAS:PDE6D vary in different cell lines, suggesting that the impact of this strategy might be cell-type-dependent. This study forms the foundation from which a potential anticancer small-molecule RAS:PDE6D complex stabilizer could be developed.
		+
		+	Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling.,Yelland T, Garcia E, Parry C, Kowalczyk D, Wojnowska M, Gohlke A, Zalar M, Cameron K, Goodwin G, Yu Q, Zhu PC, ElMaghloob Y, Pugliese A, Archibald L, Jamieson A, Chen YX, McArthur D, Bower J, Ismail S J Med Chem. 2022 Feb 10;65(3):1898-1914. doi: 10.1021/acs.jmedchem.1c01265. Epub , 2022 Feb 1. PMID:35104933<ref>PMID:35104933</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7qjk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ismail S]]		[[Category: Ismail S]]
	[[Category: Yelland T]]		[[Category: Yelland T]]

OCA at 07:03, 27 January 2022

OCA — Thu, 27 Jan 2022 07:03:28 GMT

←Older revision		Revision as of 07:03, 27 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7qjk ~~is ON HOLD~~	+	==Crystal structure of PDE6D in complex with Compound-2==
-		+	<StructureSection load='7qjk' size='340' side='right'caption='[[7qjk]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QJK FirstGlance]. <br>
-	~~Description~~:	+	</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=7qjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qjk OCA], [https://pdbe.org/7qjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qjk RCSB], [https://www.ebi.ac.uk/pdbsum/7qjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qjk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ismail S]]
		+	[[Category: Yelland T]]

OCA: Protected "7qjk" [edit=sysop:move=sysop]

OCA — Wed, 22 Dec 2021 13:59:16 GMT

Protected "7qjk" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:59, 22 December 2021

OCA: New page: '''Unreleased structure''' The entry 7qjk is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Dec 2021 13:59:15 GMT

New page: '''Unreleased structure''' The entry 7qjk is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7qjk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7qjk - Revision history

OCA at 13:18, 1 February 2024

OCA at 07:03, 27 January 2022

OCA: Protected "7qjk" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7qjk is ON HOLD Authors: Description: Category: Unreleased Structures