4xy8 - Revision history

OCA at 10:51, 10 January 2024

OCA — Wed, 10 Jan 2024 10:51:20 GMT

←Older revision		Revision as of 10:51, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xy8]] 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=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xy8]] 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=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [https://pdbe.org/4xy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [https://pdbe.org/4xy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:58, 26 April 2023

OCA — Wed, 26 Apr 2023 17:58:13 GMT

←Older revision		Revision as of 17:58, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4xy8' size='340' side='right'caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4xy8' size='340' side='right'caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xy8]] 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=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xy8]] 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=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD9, UNQ3040/PRO9856 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [https://pdbe.org/4xy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [https://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [~~http~~://pdbe.org/4xy8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN]] May play a role in chromatin remodeling and regulation of transcription.	+	[https://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN] May play a role in chromatin remodeling and regulation of transcription.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	~~[[Category: Delft, F von~~]]	+	[[Category: Edwards AM]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Filippakopoulos P]]
-	[[Category: Filippakopoulos, P]]	+	[[Category: Picaud S]]
-	[[Category: Picaud, S]]	+	[[Category: Von Delft F]]
-	[[Category: ~~Structural genomic]]~~	+
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Ligand]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 23:50, 5 June 2019

OCA — Wed, 05 Jun 2019 23:50:27 GMT

←Older revision		Revision as of 23:50, 5 June 2019
Line 1:		Line 1:

	==Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand==		==Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand==
-	<StructureSection load='4xy8' size='340' side='right' caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4xy8' size='340' side='right'caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xy8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xy8]] 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=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRD9, UNQ3040/PRO9856 ([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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [http://pdbe.org/4xy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [http://pdbe.org/4xy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:

	==See Also==		==See Also==
-	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]	+	*[[Bromodomain-containing protein 3D structures\|Bromodomain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 01:58, 10 March 2017

OCA — Fri, 10 Mar 2017 01:58:24 GMT

←Older revision		Revision as of 01:58, 10 March 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand==		==Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand==
	<StructureSection load='4xy8' size='340' side='right' caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4xy8' size='340' side='right' caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4xy8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xy8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xy8 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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [http://pdbe.org/4xy8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xy8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xy8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4xy8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bromodomain-containing protein\|Bromodomain-containing protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:50, 11 March 2015

OCA — Wed, 11 Mar 2015 11:50:08 GMT

←Older revision		Revision as of 11:50, 11 March 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand==
		+	<StructureSection load='4xy8' size='340' side='right' caption='[[4xy8]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xy8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XY8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XY8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=43U:6-(5-BROMO-2-METHOXYPHENYL)-9H-PURIN-2-AMINE'>43U</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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=4xy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xy8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xy8 RCSB], [http://www.ebi.ac.uk/pdbsum/4xy8 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BRD9_HUMAN BRD9_HUMAN]] May play a role in chromatin remodeling and regulation of transcription.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.

-	~~The entry 4xy8 is ON HOLD~~	+	9H-Purine Scaffold Reveals Induced-Fit Pocket Plasticity of the BRD9 Bromodomain.,Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P J Med Chem. 2015 Mar 5. PMID:25703523<ref>PMID:25703523</ref>

-	~~Authors: Picaud~~, S.~~, von Delft, F~~.~~, Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	[[Category: ~~Picaud~~, S]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]
-	[[Category: ~~Arrowsmith~~, ~~C.H~~]]	+	[[Category: Delft, F von]]
-	[[Category: ~~Von Delft~~, F]]	+	[[Category: Edwards, A M]]
	[[Category: Filippakopoulos, P]]		[[Category: Filippakopoulos, P]]
-	[[Category: ~~Edwards~~, ~~A.M~~]]	+	[[Category: Picaud, S]]
-	[[Category: Structural ~~Genomics Consortium (~~Sgc)]]	+	[[Category: Structural genomic]]
		+	[[Category: Bromodomain]]
		+	[[Category: Complex]]
		+	[[Category: Ligand]]
		+	[[Category: Sgc]]
		+	[[Category: Transcription]]

OCA: Protected "4xy8" [edit=sysop:move=sysop]

OCA — Thu, 12 Feb 2015 10:51:06 GMT

Protected "4xy8" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:51, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xy8 is ON HOLD Authors: Picaud, S., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortiu...

OCA — Thu, 12 Feb 2015 10:51:05 GMT

New page: '''Unreleased structure''' The entry 4xy8 is ON HOLD Authors: Picaud, S., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortiu...

New page

'''Unreleased structure'''

The entry 4xy8 is ON HOLD

Authors: Picaud, S., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

Description: Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand
[[Category: Unreleased Structures]]
[[Category: Picaud, S]]
[[Category: Bountra, C]]
[[Category: Arrowsmith, C.H]]
[[Category: Von Delft, F]]
[[Category: Filippakopoulos, P]]
[[Category: Edwards, A.M]]
[[Category: Structural Genomics Consortium (Sgc)]]