5fh6 - Revision history

OCA at 06:50, 19 July 2023

OCA — Wed, 19 Jul 2023 06:50:58 GMT

←Older revision		Revision as of 06:50, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fh6' size='340' side='right'caption='[[5fh6]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5fh6' size='340' side='right'caption='[[5fh6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fh6]] is a 4 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=5FH6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fh6]] is a 4 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=5FH6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FH6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5XM:(3~{R})-3-(PIPERIDIN-1-YLMETHYL)-2,3-DIHYDRO-1~{H}-PYRROLO[1,2-A]QUINAZOLIN-5-ONE'>5XM</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBRM1, BAF180, PB1 ([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=5XM:(3~{R})-3-(PIPERIDIN-1-YLMETHYL)-2,3-DIHYDRO-1~{H}-PYRROLO[1,2-A]QUINAZOLIN-5-ONE'>5XM</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=5fh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh6 OCA], [~~http~~://pdbe.org/5fh6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fh6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fh6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh6 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=5fh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh6 OCA], [https://pdbe.org/5fh6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fh6 RCSB], [https://www.ebi.ac.uk/pdbsum/5fh6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[~~http~~://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>	+	[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>	+	[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		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: Brennan~~, P E]]~~	+	[[Category: Brennan PE]]
-	~~[[Category: Delft, F von~~]]	+	[[Category: Edwards AM]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Fedorov O]]
-	[[Category: Fedorov, O]]	+	[[Category: Fonseca M]]
-	[[Category: Fonseca, M]]	+	[[Category: Knapp S]]
-	[[Category: Knapp, S]]	+	[[Category: Krojer T]]
-	[[Category: Krojer, T]]	+	[[Category: Ley SV]]
-	[[Category: Ley~~, S V~~]]	+	[[Category: Picaud S]]
-	[[Category: Picaud, S]]	+	[[Category: Siejka P]]
-	[[Category: Siejka, P]]	+	[[Category: Sutherell CL]]
-	[[Category: Sutherell~~, C L~~]]	+	[[Category: Tallant C]]
-	[[Category: Tallant, C]]	+	[[Category: Von Delft F]]
-	[[Category: ~~Brg1-associated factor 180]]~~	+
-	~~[[Category: Chromatin remodeling]]~~	+
-	~~[[Category: Pbrm1]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 07:19, 6 May 2020

OCA — Wed, 06 May 2020 07:19:10 GMT

←Older revision		Revision as of 07:19, 6 May 2020
Line 1:		Line 1:

	==Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10==		==Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10==
-	<StructureSection load='5fh6' size='340' side='right' caption='[[5fh6]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5fh6' size='340' side='right'caption='[[5fh6]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fh6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FH6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FH6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fh6]] is a 4 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=5FH6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FH6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XM:(3~{R})-3-(PIPERIDIN-1-YLMETHYL)-2,3-DIHYDRO-1~{H}-PYRROLO[1,2-A]QUINAZOLIN-5-ONE'>5XM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5XM:(3~{R})-3-(PIPERIDIN-1-YLMETHYL)-2,3-DIHYDRO-1~{H}-PYRROLO[1,2-A]QUINAZOLIN-5-ONE'>5XM</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=5fh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh6 OCA], [http://pdbe.org/5fh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh6 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh6 PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PBRM1, BAF180, PB1 ([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=5fh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh6 OCA], [http://pdbe.org/5fh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh6 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fh6 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 24:		Line 25:
	__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 15:44, 1 June 2016

OCA — Wed, 01 Jun 2016 15:44:32 GMT

←Older revision		Revision as of 15:44, 1 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5fh6 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10==
		+	<StructureSection load='5fh6' size='340' side='right' caption='[[5fh6]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5fh6]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FH6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FH6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5XM:(3~{R})-3-(PIPERIDIN-1-YLMETHYL)-2,3-DIHYDRO-1~{H}-PYRROLO[1,2-A]QUINAZOLIN-5-ONE'>5XM</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=5fh6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fh6 OCA], [http://pdbe.org/5fh6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fh6 RCSB], [http://www.ebi.ac.uk/pdbsum/5fh6 PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[http://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomain containing proteins PB1, SMARCA4, and SMARCA2 are important components of SWI/SNF chromatin remodeling complexes. We identified bromodomain inhibitors that target these proteins and display unusual binding modes involving water displacement from the KAc binding site. The best compound binds the fifth bromodomain of PB1 with a KD of 124 nM, SMARCA2B and SMARCA4 with KD values of 262 and 417 nM, respectively, and displays excellent selectivity over bromodomains other than PB1, SMARCA2, and SMARCA4.

-	~~Authors: Tallant~~, C., Sutherell, C~~.L.~~, ~~Siejka~~, P., ~~Krojer, T., Picaud, S., Fonseca, M.~~, Fedorov, O., ~~von Delft~~, F., ~~Arrowsmith~~, ~~C.H.~~, ~~Edwards~~, A.M.~~, Bountra, C~~.~~, Brennan, P~~.E.~~, Ley, S.V~~., ~~Knapp, S~~.	+	Identification and Development of 2,3-Dihydropyrrolo[1,2-a]quinazolin-5(1H)-one Inhibitors Targeting Bromodomains within the Switch/Sucrose Nonfermenting Complex.,Sutherell CL, Tallant C, Monteiro OP, Yapp C, Fuchs JE, Fedorov O, Siejka P, Muller S, Knapp S, Brenton JD, Brennan PE, Ley SV J Med Chem. 2016 May 26;59(10):5095-101. doi: 10.1021/acs.jmedchem.5b01997. Epub , 2016 May 11. PMID:27119626<ref>PMID:27119626</ref>

-	~~Description: Crystal structure~~ of the ~~fifth bromodomain~~ of ~~human PB1 in complex with compound 10~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5fh6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bountra, C]]
		+	[[Category: Brennan, P E]]
		+	[[Category: Delft, F von]]
		+	[[Category: Edwards, A M]]
	[[Category: Fedorov, O]]		[[Category: Fedorov, O]]
-	[[Category: Picaud, S]]
-	[[Category: Siejka, P]]
-	[[Category: Knapp, S]]
	[[Category: Fonseca, M]]		[[Category: Fonseca, M]]
		+	[[Category: Knapp, S]]
	[[Category: Krojer, T]]		[[Category: Krojer, T]]
-	[[Category: ~~Bountra~~, C]]	+	[[Category: Ley, S V]]
-	[[Category: ~~Ley~~, S.V]]	+	[[Category: Picaud, S]]
-	[[Category: ~~Arrowsmith~~, ~~C.H~~]]	+	[[Category: Siejka, P]]
-	[[Category: Sutherell, C.L]]	+	[[Category: Sutherell, C L]]
-	~~[[Category: Von Delft, F]]~~	+
-	~~[[Category: Edwards, A.M]]~~	+
-	~~[[Category: Brennan, P.E~~]]	+
	[[Category: Tallant, C]]		[[Category: Tallant, C]]
		+	[[Category: Brg1-associated factor 180]]
		+	[[Category: Chromatin remodeling]]
		+	[[Category: Pbrm1]]
		+	[[Category: Transcription]]

OCA at 18:15, 13 January 2016

OCA — Wed, 13 Jan 2016 18:15:00 GMT

←Older revision		Revision as of 18:15, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fh6 is ON HOLD	+	The entry 5fh6 is ON HOLD until Paper Publication

	Authors: Tallant, C., Sutherell, C.L., Siejka, P., Krojer, T., Picaud, S., Fonseca, M., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Ley, S.V., Knapp, S.		Authors: Tallant, C., Sutherell, C.L., Siejka, P., Krojer, T., Picaud, S., Fonseca, M., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Ley, S.V., Knapp, S.

OCA: Protected "5fh6" [edit=sysop:move=sysop]

OCA — Wed, 30 Dec 2015 17:57:00 GMT

Protected "5fh6" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:57, 30 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fh6 is ON HOLD Authors: Tallant, C., Sutherell, C.L., Siejka, P., Krojer, T., Picaud, S., Fonseca, M., Fedorov, O., von Delft, F., Arrowsmith, C.H....

OCA — Wed, 30 Dec 2015 17:56:58 GMT

New page: '''Unreleased structure''' The entry 5fh6 is ON HOLD Authors: Tallant, C., Sutherell, C.L., Siejka, P., Krojer, T., Picaud, S., Fonseca, M., Fedorov, O., von Delft, F., Arrowsmith, C.H....

New page

'''Unreleased structure'''

The entry 5fh6 is ON HOLD

Authors: Tallant, C., Sutherell, C.L., Siejka, P., Krojer, T., Picaud, S., Fonseca, M., Fedorov, O., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brennan, P.E., Ley, S.V., Knapp, S.

Description: Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10
[[Category: Unreleased Structures]]
[[Category: Fedorov, O]]
[[Category: Picaud, S]]
[[Category: Siejka, P]]
[[Category: Knapp, S]]
[[Category: Fonseca, M]]
[[Category: Krojer, T]]
[[Category: Bountra, C]]
[[Category: Ley, S.V]]
[[Category: Arrowsmith, C.H]]
[[Category: Sutherell, C.L]]
[[Category: Von Delft, F]]
[[Category: Edwards, A.M]]
[[Category: Brennan, P.E]]
[[Category: Tallant, C]]