4qbz - Revision history

OCA at 11:22, 15 February 2023

OCA — Wed, 15 Feb 2023 11:22:56 GMT

←Older revision		Revision as of 11:22, 15 February 2023
Line 3:		Line 3:
	<StructureSection load='4qbz' size='340' side='right'caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qbz' size='340' side='right'caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qbz]] is a 2 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=4QBZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qbz]] 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=4QBZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [https://pdbe.org/4qbz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [https://www.ebi.ac.uk/pdbsum/4qbz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbz ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR8 ([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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [~~http~~://pdbe.org/4qbz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qbz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TLR8_HUMAN TLR8_HUMAN]] Key component of innate and adaptive immunity. TLRs (Toll-like receptors) control host immune response against pathogens through recognition of molecular patterns specific to microorganisms. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response.<ref>PMID:17932028</ref>	+	[https://www.uniprot.org/uniprot/TLR8_HUMAN TLR8_HUMAN] Key component of innate and adaptive immunity. TLRs (Toll-like receptors) control host immune response against pathogens through recognition of molecular patterns specific to microorganisms. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response.<ref>PMID:17932028</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 20:

	==See Also==		==See Also==
-	*[[Toll-like ~~Receptors~~\|Toll-like ~~Receptors~~]]	+	*[[Toll-like Receptor 3D structures\|Toll-like Receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ohto, U]]	+	[[Category: Ohto U]]
-	[[Category: Shimizu, T]]	+	[[Category: Shimizu T]]
-	[[Category: Tanji, H]]	+	[[Category: Tanji H]]
-	~~[[Category: Antiviral and antitumor drug binding]]~~	+
-	~~[[Category: Glycosylation]]~~	+
-	~~[[Category: Innate immunity]]~~	+
-	~~[[Category: Leucine rich repeat]]~~	+
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna receptor]]~~	+
-	~~[[Category: Rna recognition]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Ssrna]]~~	+
-	~~[[Category: Structure-based ligand design]]~~	+
-	~~[[Category: Tlr8 and tlr7 agonist]]~~	+
-	~~[[Category: Vaccine adjuvant~~]]	+

OCA at 09:29, 24 April 2019

OCA — Wed, 24 Apr 2019 09:29:26 GMT

←Older revision		Revision as of 09:29, 24 April 2019
Line 1:		Line 1:

	==Crystal structure of human TLR8 in complex with DS-802==		==Crystal structure of human TLR8 in complex with DS-802==
-	<StructureSection load='4qbz' size='340' side='right' caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4qbz' size='340' side='right'caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qbz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qbz]] is a 2 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=4QBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL~~-D-~~GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-D-~~MANNOSE~~'>~~MAN~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TLR8 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://pdbe.org/4qbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbz ProSAT]</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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://pdbe.org/4qbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbz ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4qbz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4qbz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Toll-like Receptors\|Toll-like Receptors]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ohto, U]]		[[Category: Ohto, U]]
	[[Category: Shimizu, T]]		[[Category: Shimizu, T]]

OCA at 14:16, 4 August 2016

OCA — Thu, 04 Aug 2016 14:16:40 GMT

←Older revision		Revision as of 14:16, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of human TLR8 in complex with DS-802==		==Crystal structure of human TLR8 in complex with DS-802==
	<StructureSection load='4qbz' size='340' side='right' caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qbz' size='340' side='right' caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz 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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://pdbe.org/4qbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4qbz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:31, 24 December 2014

OCA — Wed, 24 Dec 2014 15:31:38 GMT

←Older revision		Revision as of 15:31, 24 December 2014
Line 7:		Line 7:
	<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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz 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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TLR8_HUMAN TLR8_HUMAN]] Key component of innate and adaptive immunity. TLRs (Toll-like receptors) control host immune response against pathogens through recognition of molecular patterns specific to microorganisms. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response.<ref>PMID:17932028</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ohto, U.]]	+	[[Category: Ohto, U]]
-	[[Category: Shimizu, T.]]	+	[[Category: Shimizu, T]]
-	[[Category: Tanji, H.]]	+	[[Category: Tanji, H]]
	[[Category: Antiviral and antitumor drug binding]]		[[Category: Antiviral and antitumor drug binding]]
	[[Category: Glycosylation]]		[[Category: Glycosylation]]

OCA at 11:43, 22 October 2014

OCA — Wed, 22 Oct 2014 11:43:53 GMT

←Older revision		Revision as of 11:43, 22 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of human TLR8 in complex with DS-802==
		+	<StructureSection load='4qbz' size='340' side='right' caption='[[4qbz]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qbz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=D80:2-BUTYL[1,3]OXAZOLO[4,5-C]QUINOLIN-4-AMINE'>D80</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qc0\|4qc0]]</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=4qbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbz RCSB], [http://www.ebi.ac.uk/pdbsum/4qbz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Toll-like receptor (TLR) 7 and 8 agonists are potential vaccine adjuvants, since they directly activate APCs and enhance Th1-driven immune responses. Previous SAR investigations in several scaffolds of small molecule TLR7/8 activators pointed to the strict dependence of the selectivity for TLR7 vis-a-vis TLR8 on the electronic configurations of the heterocyclic systems, which we sought to examine quantitatively with the goal of developing "heuristics" to define structural requisites governing activity at TLR7 and/or TLR8. We undertook a scaffold-hopping approach, entailing the syntheses and biological evaluations of 13 different chemotypes. Crystal structures of TLR8 in complex with the two most active compounds confirmed important binding interactions playing a key role in ligand occupancy and biological activity. Density functional theory based quantum chemical calculations on these compounds followed by linear discriminant analyses permitted the classification of inactive, TLR8-active, and TLR7/8 dual-active compounds, confirming the critical role of partial charges in determining biological activity.

-	~~The entry 4qbz is ON HOLD~~	+	Determinants of Activity at Human Toll-like Receptors 7 and 8: Quantitative Structure-Activity Relationship (QSAR) of Diverse Heterocyclic Scaffolds.,Yoo E, Salunke DB, Sil D, Guo X, Salyer AC, Hermanson AR, Kumar M, Malladi SS, Balakrishna R, Thompson WH, Tanji H, Ohto U, Shimizu T, David SA J Med Chem. 2014 Oct 9;57(19):7955-70. doi: 10.1021/jm500744f. Epub 2014 Sep 17. PMID:25192394<ref>PMID:25192394</ref>

-	~~Authors: Tanji~~, H., Ohto, U., Shimizu, T.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of human TLR8 in complex with DS~~-~~802~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ohto, U.]]
		+	[[Category: Shimizu, T.]]
		+	[[Category: Tanji, H.]]
		+	[[Category: Antiviral and antitumor drug binding]]
		+	[[Category: Glycosylation]]
		+	[[Category: Innate immunity]]
		+	[[Category: Leucine rich repeat]]
		+	[[Category: Rna binding]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna receptor]]
		+	[[Category: Rna recognition]]
		+	[[Category: Secreted]]
		+	[[Category: Ssrna]]
		+	[[Category: Structure-based ligand design]]
		+	[[Category: Tlr8 and tlr7 agonist]]
		+	[[Category: Vaccine adjuvant]]

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

OCA — Wed, 21 May 2014 08:16:49 GMT

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

←Older revision

Revision as of 08:16, 21 May 2014

OCA: New page: '''Unreleased structure''' The entry 4qbz is ON HOLD Authors: Tanji, H., Ohto, U., Shimizu, T. Description: Crystal structure of human TLR8 in complex with DS-802

OCA — Wed, 21 May 2014 08:16:48 GMT

New page: '''Unreleased structure''' The entry 4qbz is ON HOLD Authors: Tanji, H., Ohto, U., Shimizu, T. Description: Crystal structure of human TLR8 in complex with DS-802

New page

'''Unreleased structure'''

The entry 4qbz is ON HOLD

Authors: Tanji, H., Ohto, U., Shimizu, T.

Description: Crystal structure of human TLR8 in complex with DS-802