5ml2 - Revision history

OCA at 18:49, 1 November 2023

2023-11-01T18:49:01Z

←Older revision		Revision as of 18:49, 1 November 2023
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	<StructureSection load='5ml2' size='340' side='right'caption='[[5ml2]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5ml2' size='340' side='right'caption='[[5ml2]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ml2]] 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=5ML2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ML2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ml2]] 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=5ML2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ML2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH6:~{N}1-[(4-CHLOROPHENYL)METHYL]-~{N}1-CYCLOPENTYL-~{N}4-(PHENYLMETHYL)BENZENE-1,4-DISULFONAMIDE'>NH6</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]] 1.6Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE6D, PDED ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH6:~{N}1-[(4-CHLOROPHENYL)METHYL]-~{N}1-CYCLOPENTYL-~{N}4-(PHENYLMETHYL)BENZENE-1,4-DISULFONAMIDE'>NH6</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ml2 OCA], [~~http~~://pdbe.org/5ml2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ml2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ml2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ml2 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=5ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ml2 OCA], [https://pdbe.org/5ml2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ml2 RCSB], [https://www.ebi.ac.uk/pdbsum/5ml2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ml2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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).	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fansa~~, E K~~]]	+	[[Category: Fansa EK]]
-	[[Category: Martin-Gago, P]]	+	[[Category: Martin-Gago P]]
-	[[Category: Waldmann, H]]	+	[[Category: Waldmann H]]
-	[[Category: Wittinghofer, A]]	+	[[Category: Wittinghofer A]]
-	~~[[Category: Arl2]]~~	+
-	~~[[Category: Farnesylated-kra]]~~	+
-	~~[[Category: Lipid binding protein]]~~	+
-	~~[[Category: Plasma membrane]]~~	+
-	~~[[Category: Prenyl binding protein~~]]	+

OCA at 07:22, 19 August 2020

2020-08-19T07:22:23Z

←Older revision		Revision as of 07:22, 19 August 2020
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	==The crystal structure of PDE6D in complex with inhibitor-3==		==The crystal structure of PDE6D in complex with inhibitor-3==
-	<StructureSection load='5ml2' size='340' side='right' caption='[[5ml2]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5ml2' size='340' side='right'caption='[[5ml2]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ml2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ML2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ML2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ml2]] 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=5ML2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ML2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH6:~{N}1-[(4-CHLOROPHENYL)METHYL]-~{N}1-CYCLOPENTYL-~{N}4-(PHENYLMETHYL)BENZENE-1,4-DISULFONAMIDE'>NH6</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NH6:~{N}1-[(4-CHLOROPHENYL)METHYL]-~{N}1-CYCLOPENTYL-~{N}4-(PHENYLMETHYL)BENZENE-1,4-DISULFONAMIDE'>NH6</scene></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=5ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ml2 OCA], [http://pdbe.org/5ml2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ml2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ml2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ml2 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE6D, PDED ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ml2 OCA], [http://pdbe.org/5ml2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ml2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ml2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ml2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5ml2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ml2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Fansa, E K]]		[[Category: Fansa, E K]]
	[[Category: Martin-Gago, P]]		[[Category: Martin-Gago, P]]

OCA at 17:57, 1 February 2017

2017-02-01T17:57:32Z

←Older revision		Revision as of 17:57, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5ml2 is ~~ON HOLD until Paper~~ Publication	+	==The crystal structure of PDE6D in complex with inhibitor-3==
		+	<StructureSection load='5ml2' size='340' side='right' caption='[[5ml2]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ml2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ML2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ML2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH6:~{N}1-[(4-CHLOROPHENYL)METHYL]-~{N}1-CYCLOPENTYL-~{N}4-(PHENYLMETHYL)BENZENE-1,4-DISULFONAMIDE'>NH6</scene></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=5ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ml2 OCA], [http://pdbe.org/5ml2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ml2 RCSB], [http://www.ebi.ac.uk/pdbsum/5ml2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ml2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	Small-molecule inhibition of the interaction between the KRas oncoprotein and the chaperone PDE6delta impairs KRas spatial organization and signaling in cells. However, despite potent binding in vitro (KD <10 nm), interference with Ras signaling and growth inhibition require 5-20 mum compound concentrations. We demonstrate that these findings can be explained by fast release of high-affinity inhibitors from PDE6delta by the release factor Arl2. This limitation is overcome by novel highly selective inhibitors that bind to PDE6delta with up to 7 hydrogen bonds, resulting in picomolar affinity. Their release by Arl2 is greatly decreased, and representative compounds selectively inhibit growth of KRas mutated and -dependent cells with the highest activity recorded yet. Our findings indicate that very potent inhibitors of the KRas-PDE6delta interaction may impair the growth of tumors driven by oncogenic KRas.

-	~~Authors: Fansa, E.K~~., Martin-Gago, P., ~~Waldmann~~, H., ~~Wittinghofer~~, A.	+	A PDE6delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.,Martin-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schurmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PI, Wittinghofer A, Waldmann H Angew Chem Int Ed Engl. 2017 Jan 20. doi: 10.1002/anie.201610957. PMID:28106325<ref>PMID:28106325</ref>

-	~~Description: The crystal structure~~ of ~~PDE6D in complex with inhibitor-3~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Waldmann~~, H]]	+	<div class="pdbe-citations 5ml2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fansa, E K]]
	[[Category: Martin-Gago, P]]		[[Category: Martin-Gago, P]]
		+	[[Category: Waldmann, H]]
	[[Category: Wittinghofer, A]]		[[Category: Wittinghofer, A]]
-	[[Category: ~~Fansa, E.K~~]]	+	[[Category: Arl2]]
		+	[[Category: Farnesylated-kra]]
		+	[[Category: Lipid binding protein]]
		+	[[Category: Plasma membrane]]
		+	[[Category: Prenyl binding protein]]

OCA at 13:59, 4 January 2017

2017-01-04T13:59:51Z

←Older revision		Revision as of 13:59, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ml2 is ON HOLD	+	The entry 5ml2 is ON HOLD until Paper Publication

	Authors: Fansa, E.K., Martin-Gago, P., Waldmann, H., Wittinghofer, A.		Authors: Fansa, E.K., Martin-Gago, P., Waldmann, H., Wittinghofer, A.

OCA: Protected "5ml2" [edit=sysop:move=sysop]

2016-12-15T16:26:17Z

Protected "5ml2" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:26, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5ml2 is ON HOLD Authors: Fansa, E.K., Martin-Gago, P., Waldmann, H., Wittinghofer, A. Description: The crystal structure of PDE6D in complex with i...

2016-12-15T16:26:16Z

New page: '''Unreleased structure''' The entry 5ml2 is ON HOLD Authors: Fansa, E.K., Martin-Gago, P., Waldmann, H., Wittinghofer, A. Description: The crystal structure of PDE6D in complex with i...

New page

'''Unreleased structure'''

The entry 5ml2 is ON HOLD

Authors: Fansa, E.K., Martin-Gago, P., Waldmann, H., Wittinghofer, A.

Description: The crystal structure of PDE6D in complex with inhibitor-3
[[Category: Unreleased Structures]]
[[Category: Waldmann, H]]
[[Category: Martin-Gago, P]]
[[Category: Wittinghofer, A]]
[[Category: Fansa, E.K]]