5orb: Difference between revisions
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==Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30== | ==Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30== | ||
<StructureSection load='5orb' size='340' side='right' caption='[[5orb]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='5orb' size='340' side='right'caption='[[5orb]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5orb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ORB OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5orb]] 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=5ORB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ORB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=JR6:2-(4-methoxyphenyl)sulfanyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)ethanamide'>JR6</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.103Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=JR6:2-(4-methoxyphenyl)sulfanyl-~{N}-(2-methyl-5,6-dihydro-4~{H}-cyclopenta[c]pyrazol-3-yl)ethanamide'>JR6</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5orb OCA], [https://pdbe.org/5orb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5orb RCSB], [https://www.ebi.ac.uk/pdbsum/5orb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5orb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/BAZ2B_HUMAN BAZ2B_HUMAN] May play a role in transcriptional regulation interacting with ISWI. | ||
<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 5orb" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5orb" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Bromodomain adjacent to zinc finger 3D structures|Bromodomain adjacent to zinc finger 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Caflisch A]] | ||
[[Category: Vedove | [[Category: Dalle Vedove A]] | ||
[[Category: | [[Category: Lolli G]] | ||
[[Category: | [[Category: Marchand J-R]] | ||
Latest revision as of 19:58, 13 December 2023
Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30Crystal Structure of BAZ2B bromodomain in complex with 1-methyl-cyclopentapyrazole compound 30
Structural highlights
FunctionBAZ2B_HUMAN May play a role in transcriptional regulation interacting with ISWI. Publication Abstract from PubMedThe high-throughput docking protocol called ALTA-VS (anchor-based library tailoring virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by pre-selection of only those molecules that have optimal fragments (anchors) for the protein target. Here we present an updated version of ALTA-VS with a broader range of potential applications. The evaluation of binding energy makes use of a classical force field with implicit solvent in the continuum dielectric approximation. In about two days per protein target on a 96-core compute cluster (equipped with Xeon E3-1280 quad core processors at 2.5 GHz), the screening of a library of nearly 77 000 diverse molecules with the updated ALTA-VS protocol has resulted in the identification of 19, 3, 3, and 2 micromolar inhibitors of the human bromodomains ATAD2, BAZ2B, BRD4(1), and CREBBP, respectively. The success ratio (i.e., number of actives in a competition binding assay in vitro divided by the number of compounds tested) ranges from 8% to 13% in dose-response measurements. The poses predicted by fragment-based docking for the three ligands of the BAZ2B bromodomain were confirmed by protein X-ray crystallography. Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking.,Marchand JR, Vedove AD, Lolli G, Caflisch A J Chem Inf Model. 2017 Sep 1. doi: 10.1021/acs.jcim.7b00336. PMID:28862840[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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