5stv - Revision history

OCA at 10:04, 22 May 2024

OCA — Wed, 22 May 2024 10:04:23 GMT

←Older revision		Revision as of 10:04, 22 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5stv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5STV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5STV FirstGlance]. <br>		<table><tr><td colspan='2'>[[5stv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5STV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5STV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=V86:2-bromo-N-ethylbenzamide'>V86</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]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=V86:2-bromo-N-ethylbenzamide'>V86</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=5stv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5stv OCA], [https://pdbe.org/5stv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5stv RCSB], [https://www.ebi.ac.uk/pdbsum/5stv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5stv 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=5stv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5stv OCA], [https://pdbe.org/5stv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5stv RCSB], [https://www.ebi.ac.uk/pdbsum/5stv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5stv ProSAT]</span></td></tr>
	</table>		</table>
Line 13:		Line 14:
	The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.		The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.

-	Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites.,Barthel T, Wollenhaupt J, Lima GMA, Wahl MC, Weiss MS J Med Chem. 2022 ~~Oct 19~~. doi: 10.1021/acs.jmedchem.2c01165. PMID:36260741<ref>PMID:36260741</ref>	+	Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites.,Barthel T, Wollenhaupt J, Lima GMA, Wahl MC, Weiss MS J Med Chem. 2022 Nov 10;65(21):14630-14641. doi: 10.1021/acs.jmedchem.2c01165. , Epub 2022 Oct 19. PMID:36260741<ref>PMID:36260741</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	<div class="pdbe-citations 5stv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5stv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pre-mRNA splicing factors 3D structures\|Pre-mRNA splicing factors 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:03, 3 November 2022

OCA — Thu, 03 Nov 2022 07:03:21 GMT

←Older revision		Revision as of 07:03, 3 November 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 5stv is ~~ON HOLD~~	+	==PanDDA analysis group deposition -- Aar2/RNaseH in complex with fragment P03C11 from the F2X-Universal Library==
		+	<StructureSection load='5stv' size='340' side='right'caption='[[5stv]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5stv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5STV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5STV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=V86:2-bromo-N-ethylbenzamide'>V86</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=5stv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5stv OCA], [https://pdbe.org/5stv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5stv RCSB], [https://www.ebi.ac.uk/pdbsum/5stv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5stv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PRP8_YEAST PRP8_YEAST] Required for pre-spliceosome formation, which is the first step of pre-mRNA splicing. This protein is associated with snRNP U5. Has a role in branch site-3' splice site selection. Associates with the branch site-3' splice 3'-exon region. Also has a role in cell cycle.<ref>PMID:2835658</ref> <ref>PMID:9150140</ref> <ref>PMID:12773561</ref> <ref>PMID:18779563</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.

-	~~Authors:~~ Barthel, T., Wollenhaupt, J., Lima, G.M.A.~~, Wahl, M~~.C.~~, Weiss, M.S~~.	+	Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites.,Barthel T, Wollenhaupt J, Lima GMA, Wahl MC, Weiss MS J Med Chem. 2022 Oct 19. doi: 10.1021/acs.jmedchem.2c01165. PMID:36260741<ref>PMID:36260741</ref>

-	~~Description: PanDDA analysis group deposition --Aar2~~/~~RNaseH in complex with fragment P03C11 from~~ the ~~F2X-Universal~~ Library	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Wahl, M.C~~]]	+	<div class="pdbe-citations 5stv" style="background-color:#fffaf0;"></div>
-	[[Category: Lima~~, G.M.A~~]]	+	== References ==
-	[[Category: ~~Weiss, M.S~~]]	+	<references/>
-	[[Category: ~~Wollenhaupt, J~~]]	+	__TOC__
-	[[Category: ~~Barthel, T~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Barthel T]]
		+	[[Category: Lima GMA]]
		+	[[Category: Wahl MC]]
		+	[[Category: Weiss MS]]
		+	[[Category: Wollenhaupt J]]

OCA at 04:11, 28 September 2022

OCA — Wed, 28 Sep 2022 04:11:08 GMT

←Older revision		Revision as of 04:11, 28 September 2022
Line 3:		Line 3:
	The entry 5stv is ON HOLD		The entry 5stv is ON HOLD

-	Authors: Barthel, ~~Tatjana~~, Wollenhaupt, ~~Jan~~, Lima, ~~Gustavo~~ M.A., Wahl, ~~Markus~~ C., Weiss, ~~Manfred~~ S.	+	Authors: Barthel, T., Wollenhaupt, J., Lima, G.M.A., Wahl, M.C., Weiss, M.S.

	Description: PanDDA analysis group deposition --Aar2/RNaseH in complex with fragment P03C11 from the F2X-Universal Library		Description: PanDDA analysis group deposition --Aar2/RNaseH in complex with fragment P03C11 from the F2X-Universal Library
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Barthel, Tatjana, Wollenhaupt, Jan~~, Lima, ~~Gustavo~~ M.A]]	+	[[Category: Wahl, M.C]]
-	[[Category: ~~Wahl~~, ~~Markus C~~]]	+	[[Category: Lima, G.M.A]]
-	[[Category: ~~Weiss~~, ~~Manfred S~~]]	+	[[Category: Weiss, M.S]]
		+	[[Category: Wollenhaupt, J]]
		+	[[Category: Barthel, T]]

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

OCA — Wed, 31 Aug 2022 05:07:01 GMT

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

←Older revision

Revision as of 05:07, 31 August 2022

OCA: New page: '''Unreleased structure''' The entry 5stv is ON HOLD Authors: Barthel, Tatjana, Wollenhaupt, Jan, Lima, Gustavo M.A., Wahl, Markus C., Weiss, Manfred S. Description: PanDDA analysis gr...

OCA — Wed, 31 Aug 2022 05:07:00 GMT

New page: '''Unreleased structure''' The entry 5stv is ON HOLD Authors: Barthel, Tatjana, Wollenhaupt, Jan, Lima, Gustavo M.A., Wahl, Markus C., Weiss, Manfred S. Description: PanDDA analysis gr...

New page

'''Unreleased structure'''

The entry 5stv is ON HOLD

Authors: Barthel, Tatjana, Wollenhaupt, Jan, Lima, Gustavo M.A., Wahl, Markus C., Weiss, Manfred S.

Description: PanDDA analysis group deposition --Aar2/RNaseH in complex with fragment P03C11 from the F2X-Universal Library
[[Category: Unreleased Structures]]
[[Category: Barthel, Tatjana, Wollenhaupt, Jan, Lima, Gustavo M.A]]
[[Category: Wahl, Markus C]]
[[Category: Weiss, Manfred S]]