This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5rc2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:41, 1 March 2024) (edit) (undo)
 
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5rc2]] 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=5RC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RC2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5rc2]] 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=5RC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RC2 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=R8Y:N-ethyl-N-(thiophene-2-carbonyl)-beta-alanine'>R8Y</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]] 0.97&#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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=R8Y:N-ethyl-N-(thiophene-2-carbonyl)-beta-alanine'>R8Y</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=5rc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rc2 OCA], [https://pdbe.org/5rc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rc2 RCSB], [https://www.ebi.ac.uk/pdbsum/5rc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rc2 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=5rc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rc2 OCA], [https://pdbe.org/5rc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rc2 RCSB], [https://www.ebi.ac.uk/pdbsum/5rc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rc2 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 5rc2" 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: F2x-entry]]
+
-
[[Category: Fragmax]]
+
-
[[Category: Fragmaxapp]]
+
-
[[Category: Fragment screening]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Inhibition]]
+

Current revision

PanDDA analysis group deposition -- Endothiapepsin changed state model for fragment F2X-Entry Library E11b

PDB ID 5rc2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5rc2"
Personal tools