7t7h - Revision history

OCA at 17:01, 18 October 2023

OCA — Wed, 18 Oct 2023 17:01:08 GMT

←Older revision		Revision as of 17:01, 18 October 2023
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	<StructureSection load='7t7h' size='340' side='right'caption='[[7t7h]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='7t7h' size='340' side='right'caption='[[7t7h]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7t7h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t7h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus_Western_Reserve Vaccinia virus Western Reserve]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G7R:4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-6,7-dimethoxyquinazolin-2-amine'>G7R</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.7800026Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G7R:4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-6,7-dimethoxyquinazolin-2-amine'>G7R</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7h OCA], [https://pdbe.org/7t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7h RCSB], [https://www.ebi.ac.uk/pdbsum/7t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7h 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=7t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7h OCA], [https://pdbe.org/7t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7h RCSB], [https://www.ebi.ac.uk/pdbsum/7t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/L7QJE0_9POXV L7QJE0_9POXV]] Decapping enzyme required for the removal of the 5'-end m7GpppN cap tethered to viral and host mRNAs to allow their decay in cells. May therefore accelerate viral and cellular mRNA turnover to eliminate competing host mRNAs and allow stage-specific synthesis of viral proteins. Acceleration of the turnover of cellular transcripts may even promote the shutoff of host protein synthesis. Does not cleave unmethylated RNAs or RNAs shorter than 24 nucleotides.[ARBA:ARBA00025519]	+	[https://www.uniprot.org/uniprot/D9_VACCW D9_VACCW]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gross, J D~~]]	+	[[Category: Vaccinia virus Western Reserve]]
-	[[Category: ~~Peters, J K~~]]	+	[[Category: Gross JD]]
-	[[Category: ~~Decapping enzyme]]~~	+	[[Category: Peters JK]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Nudix]]~~	+
-	~~[[Category: Viral protein-viral protein inhibitor complex~~]]	+

OCA at 07:34, 29 June 2022

OCA — Wed, 29 Jun 2022 07:34:41 GMT

←Older revision		Revision as of 07:34, 29 June 2022
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	==Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356==		==Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356==
-	<StructureSection load='7t7h' size='340' side='right'caption='[[7t7h]]' scene=''>	+	<StructureSection load='7t7h' size='340' side='right'caption='[[7t7h]], [[Resolution\|resolution]] 1.78Å' 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=7T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7t7h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7H 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=7t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7h OCA], [https://pdbe.org/7t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7h RCSB], [https://www.ebi.ac.uk/pdbsum/7t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7h ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G7R:4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-6,7-dimethoxyquinazolin-2-amine'>G7R</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7h OCA], [https://pdbe.org/7t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7h RCSB], [https://www.ebi.ac.uk/pdbsum/7t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7h ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/L7QJE0_9POXV L7QJE0_9POXV]] Decapping enzyme required for the removal of the 5'-end m7GpppN cap tethered to viral and host mRNAs to allow their decay in cells. May therefore accelerate viral and cellular mRNA turnover to eliminate competing host mRNAs and allow stage-specific synthesis of viral proteins. Acceleration of the turnover of cellular transcripts may even promote the shutoff of host protein synthesis. Does not cleave unmethylated RNAs or RNAs shorter than 24 nucleotides.[ARBA:ARBA00025519]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vaccinia virus (VACV) represents a family of poxviruses, which possess their own decapping machinery as a part of their strategy to eliminate host mRNAs and evade the innate immune response. D9 is one of the two encoded VACV decapping enzymes that is responsible for cap removal from the 5' end of both host mRNA transcripts and viral double-stranded RNAs. Little is known about the structural requirements for D9 inhibition by small molecules. Here, we identified a minimal D9 substrate and used it to develop a real-time fluorescence assay for inhibitor discovery and characterization. We screened a panel of nucleotide-derived substrate analogues and pharmacologically active candidates to identify several compounds with nano- and low micromolar IC50 values. m(7)GpppCH2p was the most potent nucleotide inhibitor (IC50 approximately 0.08 muM), and seliciclib and CP-100356 were the most potent drug-like compounds (IC50 0.57 and 2.7 muM, respectively). The hits identified through screening inhibited D9-catalyzed decapping of 26 nt RNA substrates but were not active toward VACV D10 or human decapping enzyme, Dcp1/2. The inhibition mode for one of the compounds (CP-100356) was elucidated based on the X-ray cocrystal structure, opening the possibility for structure-based design of novel D9 inhibitors and binding probes.
		+
		+	Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9.,Bednarczyk M, Peters JK, Kasprzyk R, Starek J, Warminski M, Spiewla T, Mugridge JS, Gross JD, Jemielity J, Kowalska J ACS Chem Biol. 2022 May 16. doi: 10.1021/acschembio.2c00049. PMID:35576528<ref>PMID:35576528</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7t7h" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gross JD]]	+	[[Category: Gross, J D]]
-	[[Category: Peters JK]]	+	[[Category: Peters, J K]]
		+	[[Category: Decapping enzyme]]
		+	[[Category: Inhibitor]]
		+	[[Category: Nudix]]
		+	[[Category: Viral protein-viral protein inhibitor complex]]

OCA at 05:11, 15 June 2022

OCA — Wed, 15 Jun 2022 05:11:12 GMT

←Older revision		Revision as of 05:11, 15 June 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7t7h ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356==
-		+	<StructureSection load='7t7h' size='340' side='right'caption='[[7t7h]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7H 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=7t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7h OCA], [https://pdbe.org/7t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7h RCSB], [https://www.ebi.ac.uk/pdbsum/7t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7h ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gross JD]]
		+	[[Category: Peters JK]]

OCA at 05:57, 19 January 2022

OCA — Wed, 19 Jan 2022 05:57:03 GMT

←Older revision		Revision as of 05:57, 19 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7t7h is ON HOLD	+	The entry 7t7h is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7t7h" [edit=sysop:move=sysop]

OCA — Wed, 22 Dec 2021 14:08:31 GMT

Protected "7t7h" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:08, 22 December 2021

OCA: New page: '''Unreleased structure''' The entry 7t7h is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Dec 2021 14:08:30 GMT

New page: '''Unreleased structure''' The entry 7t7h is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7t7h is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]