5r2k - Revision history

OCA at 11:33, 21 February 2024

OCA — Wed, 21 Feb 2024 11:33:20 GMT

←Older revision		Revision as of 11:33, 21 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5r2k]] 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=5R2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>		<table><tr><td colspan='2'>[[5r2k]] 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=5R2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.029Å</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=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [https://pdbe.org/5r2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [https://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k 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=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [https://pdbe.org/5r2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [https://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5r2k" 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~~]]	+

OCA at 15:05, 8 June 2021

OCA — Tue, 08 Jun 2021 15:05:11 GMT

←Older revision		Revision as of 15:05, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='5r2k' size='340' side='right'caption='[[5r2k]], [[Resolution\|resolution]] 1.03Å' scene=''>		<StructureSection load='5r2k' size='340' side='right'caption='[[5r2k]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5r2k]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5r2k]] 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=5R2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>	+	</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [~~http~~://pdbe.org/5r2k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k 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=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [https://pdbe.org/5r2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [https://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:24, 8 July 2020

OCA — Wed, 08 Jul 2020 14:24:24 GMT

←Older revision		Revision as of 14:24, 8 July 2020
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 07, DMSO-Free==		==PanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 07, DMSO-Free==
-	<StructureSection load='5r2k' size='340' side='right'caption='[[5r2k]]' scene=''>	+	<StructureSection load='5r2k' size='340' side='right'caption='[[5r2k]], [[Resolution\|resolution]] 1.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5r2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [http://pdbe.org/5r2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [http://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k ProSAT]</span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endothiapepsin Endothiapepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.22 3.4.23.22] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [http://pdbe.org/5r2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [http://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5r2k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cryphonectria parasitica]]
		+	[[Category: Endothiapepsin]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wollenhaupt~~, ~~J, Metz~~, A, ~~Barthel, T,~~ Lima, ~~GMA, Heine~~, A, Mueller, U, ~~Klebe~~, ~~G, Weiss, MS~~]]	+	[[Category: Barthel, T]]
		+	[[Category: Heine, A]]
		+	[[Category: Klebe, G]]
		+	[[Category: Lima, G M.A]]
		+	[[Category: Metz, A]]
		+	[[Category: Mueller, U]]
		+	[[Category: Weiss, M S]]
		+	[[Category: Wollenhaupt, J]]
		+	[[Category: Hydrolase]]

OCA at 06:23, 3 June 2020

OCA — Wed, 03 Jun 2020 06:23:21 GMT

←Older revision		Revision as of 06:23, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5r2k is ON HOLD~~	+	==PanDDA analysis group deposition -- Auto-refined data of Endothiapepsin for ground state model 07, DMSO-Free==
-		+	<StructureSection load='5r2k' size='340' side='right'caption='[[5r2k]]' scene=''>
-	~~Authors: Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G., Weiss, M.S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R2K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5R2K FirstGlance]. <br>
-	~~Description:~~ PanDDA analysis group deposition --Auto-refined data of Endothiapepsin for ground state model 07, DMSO-Free	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5r2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r2k OCA], [http://pdbe.org/5r2k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5r2k RCSB], [http://www.ebi.ac.uk/pdbsum/5r2k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5r2k ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Metz, A]~~]	+	__TOC__
-	[[~~Category~~: ~~Lima, G~~.M.A]]	+	</StructureSection>
-	[~~[Category~~: ~~Mueller~~, ~~U]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Heine~~, ~~A]]~~	+	[[Category: Wollenhaupt, J, Metz, A, Barthel, T, Lima, GMA, Heine, A, Mueller, U, Klebe, G, Weiss, MS]]
-	[~~[Category~~: ~~Wollenhaupt~~, ~~J]]~~	+
-	[~~[Category~~: ~~Weiss, M~~.S]]	+
-	[[Category: ~~Klebe, G~~]]	+
-	[[Category: Barthel, T]]	+

OCA: Protected "5r2k" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2020 05:03:55 GMT

Protected "5r2k" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:03, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 5r2k is ON HOLD Authors: Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G., Weiss, M.S. Description: PanDDA a...

OCA — Wed, 19 Feb 2020 05:03:54 GMT

New page: '''Unreleased structure''' The entry 5r2k is ON HOLD Authors: Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G., Weiss, M.S. Description: PanDDA a...

New page

'''Unreleased structure'''

The entry 5r2k is ON HOLD

Authors: Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G., Weiss, M.S.

Description: PanDDA analysis group deposition --Auto-refined data of Endothiapepsin for ground state model 07, DMSO-Free
[[Category: Unreleased Structures]]
[[Category: Metz, A]]
[[Category: Lima, G.M.A]]
[[Category: Mueller, U]]
[[Category: Heine, A]]
[[Category: Wollenhaupt, J]]
[[Category: Weiss, M.S]]
[[Category: Klebe, G]]
[[Category: Barthel, T]]