6zb3: Difference between revisions

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<StructureSection load='6zb3' size='340' side='right'caption='[[6zb3]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
<StructureSection load='6zb3' size='340' side='right'caption='[[6zb3]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6zb3]] 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=6ZB3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZB3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6zb3]] 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=6ZB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZB3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=QCZ:~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide'>QCZ</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]] 1.419&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([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=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=QCZ:~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide'>QCZ</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=6zb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zb3 OCA], [http://pdbe.org/6zb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zb3 RCSB], [http://www.ebi.ac.uk/pdbsum/6zb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zb3 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=6zb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zb3 OCA], [https://pdbe.org/6zb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zb3 RCSB], [https://www.ebi.ac.uk/pdbsum/6zb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zb3 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>
[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>  
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The profound efficacy, yet associated toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (&gt;100 fold) inhibition of a sub-set of the 8 bromodomains is enticing, but challenging given the close homology. Herein, we describe the X-ray crystal structure-directed optimisation of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template (15, GSK046) was the basis for the high selectivity observed. This culminated in two tool molecules 20 (GSK620) and 56 (GSK549) which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.


The Optimisation of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor.,Seal JT, Atkinson SJ, Aylott H, Bamborough P, Chung CW, Copley RCB, Gordon LJ, Grandi P, Gray JRJ, Harrison LA, Hayhow TG, Lindon M, Messenger C, Michon AM, Mitchell DJ, Preston A, Prinjha RK, Rioja I, Taylor S, Wall ID, Watson RJ, Woolven JM, Demont EH J Med Chem. 2020 Jul 23. doi: 10.1021/acs.jmedchem.0c00796. PMID:32702236<ref>PMID:32702236</ref>
==See Also==
 
*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6zb3" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chung, C]]
[[Category: Chung C]]
[[Category: Antagonist]]
[[Category: Brd4]]
[[Category: Bromodomain]]
[[Category: Bromodomain containing protein 4]]
[[Category: Epigenetic reader]]
[[Category: Histone]]
[[Category: Inhibitor]]
[[Category: Transcription]]

Latest revision as of 10:40, 1 May 2024

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK620N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK620

Structural highlights

6zb3 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.419Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

BRD4_HUMAN Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.[1] [2]

Function

BRD4_HUMAN Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).

See Also

References

  1. ↑ French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA. BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. Cancer Res. 2003 Jan 15;63(2):304-7. PMID:12543779
  2. ↑ French CA, Miyoshi I, Aster JC, Kubonishi I, Kroll TG, Dal Cin P, Vargas SO, Perez-Atayde AR, Fletcher JA. BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t(15;19). Am J Pathol. 2001 Dec;159(6):1987-92. PMID:11733348 doi:10.1016/S0002-9440(10)63049-0

6zb3, resolution 1.42Å

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