5p1v: Difference between revisions
New page: '''Unreleased structure''' The entry 5p1v is ON HOLD Authors: Schiebel, J., Heine, A., Klebe, G. Description: Automated refinement of diffraction data obtained from an endothiapepsin c... |
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==Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 114== | |||
<StructureSection load='5p1v' size='340' side='right'caption='[[5p1v]], [[Resolution|resolution]] 1.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5p1v]] 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=5P1V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5P1V 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]] 1.301Å</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=5p1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5p1v OCA], [https://pdbe.org/5p1v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5p1v RCSB], [https://www.ebi.ac.uk/pdbsum/5p1v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5p1v ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that approximately 25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods. | |||
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.,Schiebel J, Krimmer SG, Rower K, Knorlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glockner S, Weiss MS, Mueller U, Klebe G, Heine A Structure. 2016 Aug 2;24(8):1398-409. doi: 10.1016/j.str.2016.06.010. Epub 2016, Jul 21. PMID:27452405<ref>PMID:27452405</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5p1v" style="background-color:#fffaf0;"></div> | ||
[[Category: Klebe | |||
[[Category: | ==See Also== | ||
*[[Pepsin|Pepsin]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Cryphonectria parasitica]] | |||
[[Category: Large Structures]] | |||
[[Category: Heine A]] | |||
[[Category: Klebe G]] | |||
[[Category: Schiebel J]] | |||
Latest revision as of 04:31, 28 December 2023
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 114Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 114
Structural highlights
FunctionPublication Abstract from PubMedToday the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that approximately 25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods. High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.,Schiebel J, Krimmer SG, Rower K, Knorlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glockner S, Weiss MS, Mueller U, Klebe G, Heine A Structure. 2016 Aug 2;24(8):1398-409. doi: 10.1016/j.str.2016.06.010. Epub 2016, Jul 21. PMID:27452405[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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