5rdq - Revision history

OCA at 13:43, 1 March 2024

OCA — Fri, 01 Mar 2024 13:43:48 GMT

←Older revision		Revision as of 13:43, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5rdq]] 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RDQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5rdq]] 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RDQ 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]] 1.04Å</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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [https://pdbe.org/5rdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [https://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [https://pdbe.org/5rdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [https://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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 5rdq" 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~~]]	+

OCA at 15:14, 8 June 2021

OCA — Tue, 08 Jun 2021 15:14:03 GMT

←Older revision		Revision as of 15:14, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='5rdq' size='340' side='right'caption='[[5rdq]], [[Resolution\|resolution]] 1.04Å' scene=''>		<StructureSection load='5rdq' size='340' side='right'caption='[[5rdq]], [[Resolution\|resolution]] 1.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5rdq]] 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5RDQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5rdq]] 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5RDQ 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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [~~http~~://pdbe.org/5rdq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [https://pdbe.org/5rdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [https://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:28, 17 June 2020

OCA — Wed, 17 Jun 2020 10:28:54 GMT

←Older revision		Revision as of 10:28, 17 June 2020
Line 1:		Line 1:

	==PanDDA analysis group deposition -- Endothiapepsin ground state model 42==		==PanDDA analysis group deposition -- Endothiapepsin ground state model 42==
-	<StructureSection load='5rdq' size='340' side='right'caption='[[5rdq]]' scene=''>	+	<StructureSection load='5rdq' size='340' side='right'caption='[[5rdq]], [[Resolution\|resolution]] 1.04Å' 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RDQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5rdq]] 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=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RDQ 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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [http://pdbe.org/5rdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [http://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [http://pdbe.org/5rdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [http://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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 5rdq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cryphonectria parasitica]]
		+	[[Category: Endothiapepsin]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Weiss~~, ~~MS, Wollenhaupt, J, Metz~~, A, ~~Barthel, T,~~ Lima, ~~GMA, Heine~~, A, Mueller, U, ~~Klebe~~, G]]	+	[[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: F2x-entry]]
		+	[[Category: Fragmax]]
		+	[[Category: Fragmaxapp]]
		+	[[Category: Fragment screening]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibition]]

OCA at 06:25, 3 June 2020

OCA — Wed, 03 Jun 2020 06:25:57 GMT

←Older revision		Revision as of 06:25, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5rdq is ON HOLD~~	+	==PanDDA analysis group deposition -- Endothiapepsin ground state model 42==
-		+	<StructureSection load='5rdq' size='340' side='right'caption='[[5rdq]]' scene=''>
-	~~Authors: Weiss, M.S., Wollenhaupt, J., Metz, A., Barthel, T., Lima, G.M.A., Heine, A., Mueller, U., Klebe, G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5RDQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5RDQ FirstGlance]. <br>
-	~~Description:~~ PanDDA analysis group deposition --Endothiapepsin ground state model 42	+	</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=5rdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5rdq OCA], [http://pdbe.org/5rdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5rdq RCSB], [http://www.ebi.ac.uk/pdbsum/5rdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5rdq 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: Weiss, MS, Wollenhaupt, J, Metz, A, Barthel, T, Lima, GMA, Heine, A, Mueller, U, Klebe, G]]
-	[~~[Category~~: ~~Wollenhaupt, J]~~]	+
-	[[Category: ~~Klebe, G~~]]	+
-	[[Category: Weiss, ~~M.S]]~~	+
-	~~[[Category:~~ Barthel, T]]	+

OCA at 04:32, 27 May 2020

OCA — Wed, 27 May 2020 04:32:22 GMT

←Older revision		Revision as of 04:32, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5rdq is ON HOLD ~~until sometime in the future~~	+	The entry 5rdq is ON HOLD

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

-	Description: PanDDA analysis group deposition --~~Auto-refined data of~~ Endothiapepsin ~~for~~ ground state model 42	+	Description: PanDDA analysis group deposition --Endothiapepsin ground state model 42
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Metz, A]]		[[Category: Metz, A]]
Line 12:		Line 12:
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Wollenhaupt, J]]		[[Category: Wollenhaupt, J]]
-	[[Category: Weiss, M.S]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]
		+	[[Category: Weiss, M.S]]
	[[Category: Barthel, T]]		[[Category: Barthel, T]]

OCA at 04:06, 20 May 2020

OCA — Wed, 20 May 2020 04:06:45 GMT

←Older revision		Revision as of 04:06, 20 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5rdq is ON HOLD	+	The entry 5rdq is ON HOLD until sometime in the future

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

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

OCA — Wed, 18 Mar 2020 08:13:37 GMT

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

←Older revision

Revision as of 08:13, 18 March 2020

OCA: New page: '''Unreleased structure''' The entry 5rdq 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, 18 Mar 2020 08:13:36 GMT

New page: '''Unreleased structure''' The entry 5rdq 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 5rdq 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 42
[[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]]