6bqa
From Proteopedia
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<StructureSection load='6bqa' size='340' side='right' caption='[[6bqa]], [[Resolution|resolution]] 1.03Å' scene=''> | <StructureSection load='6bqa' size='340' side='right' caption='[[6bqa]], [[Resolution|resolution]] 1.03Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6bqa]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BQA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6bqa]] 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=6BQA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BQA FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=67C:3-[6-(BUT-3-EN-1-YL)-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-C]PYRIDIN-4-YL]-N,N-DIMETHYLBENZAMIDE'>67C</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=67C:3-[6-(BUT-3-EN-1-YL)-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-C]PYRIDIN-4-YL]-N,N-DIMETHYLBENZAMIDE'>67C</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6bqd|6bqd]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6bqd|6bqd]]</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=6bqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bqa OCA], [http://pdbe.org/6bqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bqa RCSB], [http://www.ebi.ac.uk/pdbsum/6bqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bqa 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=6bqa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bqa OCA], [http://pdbe.org/6bqa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bqa RCSB], [http://www.ebi.ac.uk/pdbsum/6bqa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bqa 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. | [[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 == | ||
| + | Targeting the interaction with or displacement of the 'right' water molecule can significantly increase inhibitor potency in structure-guided drug design. Multiple computational approaches exist to predict which waters should be targeted for displacement to achieve the largest gain in potency. However, the relative success of different methods remains underexplored. Here, we present a comparison of the ability of five water prediction programs (3D-RISM, SZMAP, WaterFLAP, WaterRank, and WaterMap) to predict crystallographic water locations, calculate their binding free energies, and to relate differences in these energies to observed changes in potency. The structural cohort included nine Bruton's Tyrosine Kinase (BTK) structures, and nine bromodomain structures. Each program accurately predicted the locations of most crystallographic water molecules. However, the predicted binding free energies correlated poorly with the observed changes in inhibitor potency when solvent atoms were displaced by chemical changes in closely related compounds. | ||
| + | |||
| + | Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.,Nittinger E, Gibbons P, Eigenbrot C, Davies DR, Maurer B, Yu CL, Kiefer JR, Kuglstatter A, Murray J, Ortwine DF, Tang Y, Tsui V J Comput Aided Mol Des. 2019 Feb 12. pii: 10.1007/s10822-019-00187-y. doi:, 10.1007/s10822-019-00187-y. PMID:30756207<ref>PMID:30756207</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6bqa" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Human]] | ||
[[Category: Murray, J M]] | [[Category: Murray, J M]] | ||
[[Category: Tang, Y]] | [[Category: Tang, Y]] | ||
Revision as of 15:54, 27 February 2019
BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide
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Categories: Human | Murray, J M | Tang, Y | Brd9 | Bromodomain | Gene regulation
