5lrl: Difference between revisions

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'''Unreleased structure'''


The entry 5lrl is ON HOLD  until Paper Publication
==CRYSTAL STRUCTURE OF HSP90 IN COMPLEX WITH A003492875==
<StructureSection load='5lrl' size='340' side='right'caption='[[5lrl]], [[Resolution|resolution]] 1.33&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5lrl]] 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=5LRL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LRL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.33&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=73S:2-azanyl-5-chloranyl-~{N}-[(9~{R})-4-(1~{H}-imidazo[4,5-c]pyridin-2-yl)-9~{H}-fluoren-9-yl]pyrimidine-4-carboxamide'>73S</scene></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=5lrl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lrl OCA], [https://pdbe.org/5lrl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lrl RCSB], [https://www.ebi.ac.uk/pdbsum/5lrl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lrl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HS90A_HUMAN HS90A_HUMAN] Molecular chaperone that promotes the maturation, structural maintenance and proper regulation of specific target proteins involved for instance in cell cycle control and signal transduction. Undergoes a functional cycle that is linked to its ATPase activity. This cycle probably induces conformational changes in the client proteins, thereby causing their activation. Interacts dynamically with various co-chaperones that modulate its substrate recognition, ATPase cycle and chaperone function.<ref>PMID:15937123</ref> <ref>PMID:11274138</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We here report on nonequilibrium targeted molecular dynamics simulations as a tool for the estimation of protein-ligand unbinding kinetics. Correlating simulations with experimental data from SPR kinetics measurements and X-ray crystallography on two small molecule compound libraries bound to the N-terminal domain of the chaperone Hsp90, we show that the mean nonequilibrium work computed in an ensemble of trajectories of enforced ligand unbinding is a promising predictor for ligand unbinding rates. We furthermore investigate the molecular basis determining unbinding rates within the compound libraries. We propose ligand conformational changes and protein-ligand nonbonded interactions to impact on unbinding rates. Ligands may remain longer at the protein if they exhibit strong electrostatic and/or van der Waals interactions with the target. In the case of ligands with a rigid chemical scaffold that exhibit longer residence times, transient electrostatic interactions with the protein appear to facilitate unbinding. Our results imply that understanding the unbinding pathway and the protein-ligand interactions along this path is crucial for the prediction of small molecule ligands with defined unbinding kinetics.


Authors: VALLEE, F., DUPUY, A.
Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations.,Wolf S, Amaral M, Lowinski M, Vallee F, Musil D, Guldenhaupt J, Dreyer MK, Bomke J, Frech M, Schlitter J, Gerwert K J Chem Inf Model. 2019 Dec 23;59(12):5135-5147. doi: 10.1021/acs.jcim.9b00592., Epub 2019 Nov 22. PMID:31697501<ref>PMID:31697501</ref>


Description: CRYSTAL STRUCTURE OF HSP90 IN COMPLEX WITH A003492875
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Dupuy, A]]
<div class="pdbe-citations 5lrl" style="background-color:#fffaf0;"></div>
[[Category: Vallee, F]]
 
==See Also==
*[[Heat Shock Protein structures|Heat Shock Protein structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Dupuy A]]
[[Category: Vallee F]]
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