5r2d: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5r2d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R2D FirstGlance]. <br>
<table><tr><td colspan='2'>[[5r2d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R2D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=REG:1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea'>REG</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]] 0.919&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=REG:1-cyclopentyl-3-[[(2~{S})-oxolan-2-yl]methyl]urea'>REG</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=5r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2d OCA], [https://pdbe.org/5r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r2d RCSB], [https://www.ebi.ac.uk/pdbsum/5r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2d 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=5r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2d OCA], [https://pdbe.org/5r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r2d RCSB], [https://www.ebi.ac.uk/pdbsum/5r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.


F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening.,Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS Structure. 2020 Jun 2;28(6):694-706.e5. doi: 10.1016/j.str.2020.04.019. Epub 2020, May 14. PMID:32413289<ref>PMID:32413289</ref>
==See Also==
 
*[[Pepsin|Pepsin]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5r2d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cryphonectria parasitica]]
[[Category: Cryphonectria parasitica]]
[[Category: Endothiapepsin]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Barthel, T]]
[[Category: Barthel T]]
[[Category: Heine, A]]
[[Category: Heine A]]
[[Category: Klebe, G]]
[[Category: Klebe G]]
[[Category: Lima, G M.A]]
[[Category: Lima GMA]]
[[Category: Metz, A]]
[[Category: Metz A]]
[[Category: Mueller, U]]
[[Category: Mueller U]]
[[Category: Weiss, M S]]
[[Category: Weiss MS]]
[[Category: Wollenhaupt, J]]
[[Category: Wollenhaupt J]]
[[Category: Hydrolase]]

Latest revision as of 14:33, 21 February 2024

PanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry H11, DMSO-freePanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry H11, DMSO-free

Structural highlights

5r2d is a 1 chain structure with sequence from Cryphonectria parasitica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.919Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CARP_CRYPA

See Also

5r2d, resolution 0.92Å

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