5ngr - Revision history

OCA at 12:56, 15 November 2023

OCA — Wed, 15 Nov 2023 12:56:08 GMT

←Older revision		Revision as of 12:56, 15 November 2023
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	<StructureSection load='5ngr' size='340' side='right'caption='[[5ngr]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5ngr' size='340' side='right'caption='[[5ngr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ngr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NGR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ngr]] 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=5NGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NGR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8WT:8-methylsulfanyl-7~{H}-purin-6-amine'>8WT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ngs\|5ngs]], [[5ngt\|5ngt]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8WT:8-methylsulfanyl-7~{H}-purin-6-amine'>8WT</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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ngr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngr OCA], [~~http~~://pdbe.org/5ngr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ngr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ngr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngr 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=5ngr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngr OCA], [https://pdbe.org/5ngr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ngr RCSB], [https://www.ebi.ac.uk/pdbsum/5ngr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>	+	[https://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>
	<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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Almlof, I]]	+	[[Category: Almlof I]]
-	~~[[Category: Berglund, U Warpman~~]]	+	[[Category: Carlsson J]]
-	[[Category: Carlsson, J]]	+	[[Category: Gustafsson R]]
-	[[Category: Gustafsson, R]]	+	[[Category: Helleday T]]
-	[[Category: Helleday, T]]	+	[[Category: Homan E]]
-	[[Category: Homan, E]]	+	[[Category: Rudling A]]
-	[[Category: Rudling, A]]	+	[[Category: Scobie M]]
-	[[Category: Scobie, M]]	+	[[Category: Stenmark P]]
-	[[Category: Stenmark, P]]	+	[[Category: Warpman Berglund U]]
-	[[Category: ~~Fragment]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Oxidised nucleotide~~]]	+

OCA at 12:04, 26 August 2020

OCA — Wed, 26 Aug 2020 12:04:11 GMT

←Older revision		Revision as of 12:04, 26 August 2020
Line 1:		Line 1:

	==Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-amine==		==Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-amine==
-	<StructureSection load='5ngr' size='340' side='right' caption='[[5ngr]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5ngr' size='340' side='right'caption='[[5ngr]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ngr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NGR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ngr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NGR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NGR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8WT:8-methylsulfanyl-7~{H}-purin-6-amine'>8WT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8WT:8-methylsulfanyl-7~{H}-purin-6-amine'>8WT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ngs\|5ngs]], [[5ngt\|5ngt]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ngs\|5ngs]], [[5ngt\|5ngt]]</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=5ngr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngr OCA], [http://pdbe.org/5ngr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ngr RCSB], [http://www.ebi.ac.uk/pdbsum/5ngr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngr ProSAT]</span></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=5ngr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngr OCA], [http://pdbe.org/5ngr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ngr RCSB], [http://www.ebi.ac.uk/pdbsum/5ngr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5ngr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ngr" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures\|7%2C8-dihydro-8-oxoguanine triphosphatase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Almlof, I]]		[[Category: Almlof, I]]
	[[Category: Berglund, U Warpman]]		[[Category: Berglund, U Warpman]]

OCA at 09:07, 4 October 2017

OCA — Wed, 04 Oct 2017 09:07:50 GMT

←Older revision		Revision as of 09:07, 4 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ngr is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human MTH1 in complex with fragment inhibitor 8-(methylsulfanyl)-7H-purin-6-amine==
		+	<StructureSection load='5ngr' size='340' side='right' caption='[[5ngr]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ngr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NGR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8WT:8-methylsulfanyl-7~{H}-purin-6-amine'>8WT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ngs\|5ngs]], [[5ngt\|5ngt]]</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=5ngr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ngr OCA], [http://pdbe.org/5ngr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ngr RCSB], [http://www.ebi.ac.uk/pdbsum/5ngr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ngr ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/8ODP_HUMAN 8ODP_HUMAN]] Antimutagenic. Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress. Hydrolyzes 8-oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions. Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP.<ref>PMID:10373420</ref> <ref>PMID:10608900</ref> <ref>PMID:11139615</ref> <ref>PMID:12857738</ref> <ref>PMID:22556419</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Fragment-based lead discovery has emerged as a leading drug development strategy for novel therapeutic targets. Although fragment-based drug discovery benefits immensely from access to atomic-resolution information, structure-based virtual screening has rarely been used to drive fragment discovery and optimization. Here, molecular docking of 0.3 million fragments to a crystal structure of cancer target MTH1 was performed. Twenty-two predicted fragment ligands, for which analogs could be acquired commercially, were experimentally evaluated. Five fragments inhibited MTH1 with IC50 values ranging from 6 to 79 muM. Structure-based optimization guided by predicted binding modes and analogs from commercial chemical libraries yielded nanomolar inhibitors. Subsequently solved crystal structures confirmed binding modes predicted by docking for three scaffolds. Structure-guided exploration of commercial chemical space using molecular docking gives access to fragment libraries that are several orders of magnitude larger than those screened experimentally and can enable efficient optimization of hits to potent leads.

-	~~Authors~~:	+	Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space.,Rudling A, Gustafsson R, Almlof I, Homan E, Scobie M, Warpman Berglund U, Helleday T, Stenmark P, Carlsson J J Med Chem. 2017 Oct 3. doi: 10.1021/acs.jmedchem.7b01006. PMID:28929756<ref>PMID:28929756</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ngr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Almlof, I]]
		+	[[Category: Berglund, U Warpman]]
		+	[[Category: Carlsson, J]]
		+	[[Category: Gustafsson, R]]
		+	[[Category: Helleday, T]]
		+	[[Category: Homan, E]]
		+	[[Category: Rudling, A]]
		+	[[Category: Scobie, M]]
		+	[[Category: Stenmark, P]]
		+	[[Category: Fragment]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Oxidised nucleotide]]

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

OCA — Wed, 05 Apr 2017 10:06:30 GMT

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

←Older revision

Revision as of 10:06, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5ngr is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 10:06:29 GMT

New page: '''Unreleased structure''' The entry 5ngr is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5ngr is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]