3wz8 - Revision history

OCA at 13:35, 8 November 2023

OCA — Wed, 08 Nov 2023 13:35:09 GMT

←Older revision		Revision as of 13:35, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3wz8]] 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=3WZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WZ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3wz8]] 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=3WZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WZ8 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=IXV:N-BENZYL-4-PHENYL-2-[(N-PHENYL-BETA-ALANYL)AMINO]THIOPHENE-3-CARBOXAMIDE'>IXV</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.45Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wz6\|3wz6]], [[3wz7\|3wz7]]</div></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=IXV:N-BENZYL-4-PHENYL-2-[(N-PHENYL-BETA-ALANYL)AMINO]THIOPHENE-3-CARBOXAMIDE'>IXV</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [https://pdbe.org/3wz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [https://www.ebi.ac.uk/pdbsum/3wz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz8 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=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [https://pdbe.org/3wz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [https://www.ebi.ac.uk/pdbsum/3wz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz8 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
-	[[Category: Endothiapepsin]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Diederich~~, W E~~]]	+	[[Category: Diederich WE]]
-	[[Category: Kuhnert, M]]	+	[[Category: Kuhnert M]]
-	[[Category: Steuber, H]]	+	[[Category: Steuber H]]
-	~~[[Category: Aspartic protease]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 05:36, 10 August 2022

OCA — Wed, 10 Aug 2022 05:36:21 GMT

←Older revision		Revision as of 05:36, 10 August 2022
Line 1:		Line 1:

	==Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)==		==Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)==
-	<StructureSection load='3wz8' size='340' side='right' caption='[[3wz8]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='3wz8' size='340' side='right'caption='[[3wz8]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wz8]] 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=3WZ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wz8]] 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=3WZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IXV:N-BENZYL-4-PHENYL-2-[(N-PHENYL-BETA-ALANYL)AMINO]THIOPHENE-3-CARBOXAMIDE'>IXV</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</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=IXV:N-BENZYL-4-PHENYL-2-[(N-PHENYL-BETA-ALANYL)AMINO]THIOPHENE-3-CARBOXAMIDE'>IXV</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wz6\|3wz6]], [[3wz7\|3wz7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wz6\|3wz6]], [[3wz7\|3wz7]]</div></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='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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [~~http~~://pdbe.org/3wz8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wz8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz8 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=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [https://pdbe.org/3wz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [https://www.ebi.ac.uk/pdbsum/3wz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 3wz8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3wz8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pepsin\|Pepsin]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
		+	[[Category: Large Structures]]
	[[Category: Diederich, W E]]		[[Category: Diederich, W E]]
	[[Category: Kuhnert, M]]		[[Category: Kuhnert, M]]

OCA at 13:22, 10 May 2017

OCA — Wed, 10 May 2017 13:22:43 GMT

←Older revision		Revision as of 13:22, 10 May 2017
Line 1:		Line 1:
		+
	==Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)==		==Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)==
	<StructureSection load='3wz8' size='340' side='right' caption='[[3wz8]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='3wz8' size='340' side='right' caption='[[3wz8]], [[Resolution\|resolution]] 1.45Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wz6\|3wz6]], [[3wz7\|3wz7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wz6\|3wz6]], [[3wz7\|3wz7]]</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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [http://www.ebi.ac.uk/pdbsum/3wz8 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [http://pdbe.org/3wz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [http://www.ebi.ac.uk/pdbsum/3wz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wz8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3wz8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:03, 5 August 2015

OCA — Wed, 05 Aug 2015 20:03:05 GMT

←Older revision		Revision as of 20:03, 5 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)==
		+	<StructureSection load='3wz8' size='340' side='right' caption='[[3wz8]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wz8]] 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=3WZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WZ8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IXV:N-BENZYL-4-PHENYL-2-[(N-PHENYL-BETA-ALANYL)AMINO]THIOPHENE-3-CARBOXAMIDE'>IXV</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wz6\|3wz6]], [[3wz7\|3wz7]]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wz8 RCSB], [http://www.ebi.ac.uk/pdbsum/3wz8 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Successful lead optimization in structure-based drug discovery depends on the correct deduction and interpretation of the underlying structure-activity relationships (SAR) to facilitate efficient decision-making on the next candidates to be synthesized. Consequently, the question arises, how frequently a binding mode (re)-validation is required, to ensure not to be misled by invalid assumptions on the binding geometry. We present an example in which minor chemical modifications within one inhibitor series lead to surprisingly different binding modes. X-ray structure determination of eight inhibitors derived from one core scaffold resulted in four different binding modes in the aspartic protease endothiapepsin, a well-established surrogate for e.g. renin and beta-secretase. In addition, we suggest an empirical metrics that might serve as an indicator during lead optimization to qualify compounds as candidates for structural revalidation.

-	~~The entry 3wz8 is ON HOLD until Paper Publication~~	+	Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors.,Kuhnert M, Koster H, Bartholomaus R, Park AY, Shahim A, Heine A, Steuber H, Klebe G, Diederich WE Angew Chem Int Ed Engl. 2015 Feb 23;54(9):2849-53. doi: 10.1002/anie.201411206., Epub 2015 Jan 28. PMID:25630461<ref>PMID:25630461</ref>

-	~~Authors: Kuhnert~~, M.~~, Steuber, H~~.~~, Diederich, W.E~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: Endothiapepsin ~~in complex with Gewald reaction-derived inhibitor (8)~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cryphonectria parasitica]]
		+	[[Category: Endothiapepsin]]
		+	[[Category: Diederich, W E]]
	[[Category: Kuhnert, M]]		[[Category: Kuhnert, M]]
	[[Category: Steuber, H]]		[[Category: Steuber, H]]
-	[[Category: ~~Diederich, W.E~~]]	+	[[Category: Aspartic protease]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 13:08, 24 December 2014

OCA — Wed, 24 Dec 2014 13:08:25 GMT

←Older revision		Revision as of 13:08, 24 December 2014
Line 6:		Line 6:

	Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)		Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)
		+	[[Category: Unreleased Structures]]
		+	[[Category: Kuhnert, M]]
		+	[[Category: Steuber, H]]
		+	[[Category: Diederich, W.E]]

OCA at 06:04, 8 October 2014

OCA — Wed, 08 Oct 2014 06:04:15 GMT

←Older revision		Revision as of 06:04, 8 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wz8 is ON HOLD	+	The entry 3wz8 is ON HOLD until Paper Publication

-	Authors: Kuhnert, M., Steuber, H., Diederich, W. E.	+	Authors: Kuhnert, M., Steuber, H., Diederich, W.E.

	Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)		Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)

OCA: Protected "3wz8" [edit=sysop:move=sysop]

OCA — Wed, 24 Sep 2014 07:38:25 GMT

Protected "3wz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:38, 24 September 2014

OCA: New page: '''Unreleased structure''' The entry 3wz8 is ON HOLD Authors: Kuhnert, M., Steuber, H., Diederich, W. E. Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (...

OCA — Wed, 24 Sep 2014 07:38:23 GMT

New page: '''Unreleased structure''' The entry 3wz8 is ON HOLD Authors: Kuhnert, M., Steuber, H., Diederich, W. E. Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (...

New page

'''Unreleased structure'''

The entry 3wz8 is ON HOLD

Authors: Kuhnert, M., Steuber, H., Diederich, W. E.

Description: Endothiapepsin in complex with Gewald reaction-derived inhibitor (8)