5o5f - Revision history

OCA at 19:08, 29 November 2023

2023-11-29T19:08:43Z

←Older revision		Revision as of 19:08, 29 November 2023
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	==Crystal structure of the human BRPF1 bromodomain in complex with BZ038==		==Crystal structure of the human BRPF1 bromodomain in complex with BZ038==
-	<StructureSection load='5o5f' size='340' side='right' caption='[[5o5f]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='5o5f' size='340' side='right'caption='[[5o5f]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5f]] 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=5O5F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5O5F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5f]] 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=5O5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5O5F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9LT:1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide'>9LT</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 1.302Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRPF1, BR140 ([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=9LT:1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide'>9LT</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=5o5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5f OCA], [~~http~~://pdbe.org/5o5f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5o5f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5o5f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5f 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=5o5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5f OCA], [https://pdbe.org/5o5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5o5f RCSB], [https://www.ebi.ac.uk/pdbsum/5o5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BRPF1_HUMAN BRPF1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.<ref>PMID:16387653</ref> <ref>PMID:18794358</ref>	+	[https://www.uniprot.org/uniprot/BRPF1_HUMAN BRPF1_HUMAN] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.<ref>PMID:16387653</ref> <ref>PMID:18794358</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5o5f" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5o5f" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Peregrin\|Peregrin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Caflisch, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zhu, J~~]]	+	[[Category: Caflisch A]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Zhu J]]
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 05:49, 27 June 2018

2018-06-27T05:49:43Z

←Older revision		Revision as of 05:49, 27 June 2018
Line 3:		Line 3:
	<StructureSection load='5o5f' size='340' side='right' caption='[[5o5f]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='5o5f' size='340' side='right' caption='[[5o5f]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5o5f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5o5f]] 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=5O5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9LT:1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide'>9LT</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9LT:1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide'>9LT</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRPF1, BR140 ([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=5o5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5f OCA], [http://pdbe.org/5o5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5f RCSB], [http://www.ebi.ac.uk/pdbsum/5o5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5f 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=5o5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5f OCA], [http://pdbe.org/5o5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5f RCSB], [http://www.ebi.ac.uk/pdbsum/5o5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BRPF1_HUMAN BRPF1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.<ref>PMID:16387653</ref> <ref>PMID:18794358</ref>		[[http://www.uniprot.org/uniprot/BRPF1_HUMAN BRPF1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.<ref>PMID:16387653</ref> <ref>PMID:18794358</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bromodomain and plant homeodomain (PHD) finger containing protein 1 (BRPF1) is a member of subfamily IV of the human bromodomains. Experimental evidence suggests that BRPF1 is involved in leukemia. In a previous high-throughput docking campaign we identified several chemotypes targeting the BRPF1 bromodomain. Here, pharmacophore searches using the binding modes of two of these chemotypes resulted in two new series of ligands of the BRPF1 bromodomain. The 2,3-dioxo-quinoxaline 21 exhibits a 2-muM affinity for the BRPF1 bromodomain in two different competition binding assays, and more than 100-fold selectivity for BRPF1 against other members of subfamily IV and representatives of other subfamilies. Cellular activity is confirmed by a viability assay in a leukemia cell line. Isothermal titration calorimetry measurements reveal enthalpy-driven binding for compounds 21, 26 (KD=3muM), and the 2,4-dimethyl-oxazole derivative 42 (KD=10muM). Multiple molecular dynamics simulations and a dozen co-crystal structures at high resolution provide useful information for further optimization of affinity for the BRPF1 bromodomain.
		+
		+	Structure-based discovery of selective BRPF1 bromodomain inhibitors.,Zhu J, Zhou C, Caflisch A Eur J Med Chem. 2018 Jun 2;155:337-352. doi: 10.1016/j.ejmech.2018.05.037. PMID:29902720<ref>PMID:29902720</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5o5f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
	[[Category: Zhu, J]]		[[Category: Zhu, J]]

OCA at 07:29, 14 June 2018

2018-06-14T07:29:38Z

←Older revision		Revision as of 07:29, 14 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5o5f is ~~ON HOLD~~	+	==Crystal structure of the human BRPF1 bromodomain in complex with BZ038==
-		+	<StructureSection load='5o5f' size='340' side='right' caption='[[5o5f]], [[Resolution\|resolution]] 1.30Å' scene=''>
-	~~Authors~~: ~~Zhu~~, J., ~~Caflisch~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5o5f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5O5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5O5F FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of the ~~human BRPF1 bromodomain in~~ complex ~~with BZ038~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9LT:1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide'>9LT</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5o5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5o5f OCA], [http://pdbe.org/5o5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5o5f RCSB], [http://www.ebi.ac.uk/pdbsum/5o5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5o5f ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BRPF1_HUMAN BRPF1_HUMAN]] Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. Positively regulates the transcription of RUNX1 and RUNX2.<ref>PMID:16387653</ref> <ref>PMID:18794358</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Caflisch, A]]
	[[Category: Zhu, J]]		[[Category: Zhu, J]]
-	[[Category: ~~Caflisch, A~~]]	+	[[Category: Dna binding protein]]
		+	[[Category: Inhibitor]]
		+	[[Category: Transcription]]

OCA: Protected "5o5f" [edit=sysop:move=sysop]

2017-09-27T12:03:28Z

Protected "5o5f" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5o5f is ON HOLD Authors: Zhu, J., Caflisch, A. Description: Crystal structure of the human BRPF1 bromodomain in complex with BZ038 [[Category: Unre...

2017-09-27T12:03:26Z

New page: '''Unreleased structure''' The entry 5o5f is ON HOLD Authors: Zhu, J., Caflisch, A. Description: Crystal structure of the human BRPF1 bromodomain in complex with BZ038 [[Category: Unre...

New page

'''Unreleased structure'''

The entry 5o5f is ON HOLD

Authors: Zhu, J., Caflisch, A.

Description: Crystal structure of the human BRPF1 bromodomain in complex with BZ038
[[Category: Unreleased Structures]]
[[Category: Zhu, J]]
[[Category: Caflisch, A]]