4y5g - Revision history

OCA at 10:53, 10 January 2024

OCA — Wed, 10 Jan 2024 10:53:02 GMT

←Older revision		Revision as of 10:53, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=47U:N-(PYRIDIN-2-YL)-2-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)ACETAMIDE'>47U</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.47Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=47U:N-(PYRIDIN-2-YL)-2-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)ACETAMIDE'>47U</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [https://pdbe.org/4y5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [https://www.ebi.ac.uk/pdbsum/4y5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y5g 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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [https://pdbe.org/4y5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [https://www.ebi.ac.uk/pdbsum/4y5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y5g ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:59, 3 May 2023

OCA — Wed, 03 May 2023 07:59:24 GMT

←Older revision		Revision as of 07:59, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4y5g' size='340' side='right'caption='[[4y5g]], [[Resolution\|resolution]] 1.47Å' scene=''>		<StructureSection load='4y5g' size='340' side='right'caption='[[4y5g]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=47U:N-(PYRIDIN-2-YL)-2-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)ACETAMIDE'>47U</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=47U:N-(PYRIDIN-2-YL)-2-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)ACETAMIDE'>47U</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pgi\|3pgi]], [[4y35\|4y35]], [[4y36\|4y36]], [[4y37\|4y37]], [[4y39\|4y39]], [[4y3a\|4y3a]], [[4y3d\|4y3d]], [[4y3f\|4y3f]], [[4y3g\|4y3g]], [[4y3l\|4y3l]], [[4y3m\|4y3m]], [[4y3n\|4y3n]], [[4y3p\|4y3p]], [[4y3q\|4y3q]], [[4y3r\|4y3r]], [[4y3s\|4y3s]], [[4y3t\|4y3t]], [[4y3w\|4y3w]], [[4y3x\|4y3x]], [[4y3z\|4y3z]], [[4y41\|4y41]], [[4y43\|4y43]], [[4y44\|4y44]], [[4y45\|4y45]], [[4y47\|4y47]], [[4y4a\|4y4a]], [[4y4b\|4y4b]], [[4y4c\|4y4c]], [[4y4e\|4y4e]], [[4y4t\|4y4t]], [[4y4u\|4y4u]], [[4y4w\|4y4w]], [[4y4x\|4y4x]], [[4y4z\|4y4z]], [[4y50\|4y50]], [[4y51\|4y51]], [[4y53\|4y53]], [[4y54\|4y54]], [[4y56\|4y56]], [[4y57\|4y57]], [[4y58\|4y58]], [[4y5a\|4y5a]], [[4y5b\|4y5b]], [[4y5c\|4y5c]], [[4y5e\|4y5e]], [[4y5k\|4y5k]], [[4y5l\|4y5l]], [[4y5m\|4y5m]], [[4y5n\|4y5n]], [[4y5p\|4y5p]], [[4yck\|4yck]], [[4yct\|4yct]], [[4ycy\|4ycy]], [[4yd3\|4yd3]], [[4yd4\|4yd4]], [[4yd5\|4yd5]], [[4yd6\|4yd6]], [[4yd7\|4yd7]], [[4y48\|4y48]], [[4y4j\|4y4j]], [[4y4g\|4y4g]], [[4y4d\|4y4d]], [[4y38\|4y38]], [[4y3y\|4y3y]], [[4y3j\|4y3j]]</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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [https://pdbe.org/4y5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [https://www.ebi.ac.uk/pdbsum/4y5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y5g ProSAT]</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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [~~http~~://pdbe.org/4y5g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y5g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y5g 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]
-	~~Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3)~~. ~~They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer~~. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.	+

-	A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes.,Koster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G J Med Chem. 2011 Oct 25. PMID:21972967<ref>PMID:21972967</ref>	+	==See Also==
-		+	*[[Pepsin\|Pepsin]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 4y5g" 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: Heine, A]]	+	[[Category: Heine A]]
-	[[Category: Klebe, G]]	+	[[Category: Klebe G]]
-	[[Category: Wang, X]]	+	[[Category: Wang X]]
-	~~[[Category: Aspartic protease]]~~	+
-	~~[[Category: Fragment screening]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibition~~]]	+

OCA at 00:27, 6 June 2019

OCA — Thu, 06 Jun 2019 00:27:11 GMT

←Older revision		Revision as of 00:27, 6 June 2019
Line 1:		Line 1:

	==Endothiapepsin in complex with fragment 272==		==Endothiapepsin in complex with fragment 272==
-	<StructureSection load='4y5g' size='340' side='right' caption='[[4y5g]], [[Resolution\|resolution]] 1.47Å' scene=''>	+	<StructureSection load='4y5g' size='340' side='right'caption='[[4y5g]], [[Resolution\|resolution]] 1.47Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pgi\|3pgi]], [[4y35\|4y35]], [[4y36\|4y36]], [[4y37\|4y37]], [[4y39\|4y39]], [[4y3a\|4y3a]], [[4y3d\|4y3d]], [[4y3f\|4y3f]], [[4y3g\|4y3g]], [[4y3l\|4y3l]], [[4y3m\|4y3m]], [[4y3n\|4y3n]], [[4y3p\|4y3p]], [[4y3q\|4y3q]], [[4y3r\|4y3r]], [[4y3s\|4y3s]], [[4y3t\|4y3t]], [[4y3w\|4y3w]], [[4y3x\|4y3x]], [[4y3z\|4y3z]], [[4y41\|4y41]], [[4y43\|4y43]], [[4y44\|4y44]], [[4y45\|4y45]], [[4y47\|4y47]], [[4y4a\|4y4a]], [[4y4b\|4y4b]], [[4y4c\|4y4c]], [[4y4e\|4y4e]], [[4y4t\|4y4t]], [[4y4u\|4y4u]], [[4y4w\|4y4w]], [[4y4x\|4y4x]], [[4y4z\|4y4z]], [[4y50\|4y50]], [[4y51\|4y51]], [[4y53\|4y53]], [[4y54\|4y54]], [[4y56\|4y56]], [[4y57\|4y57]], [[4y58\|4y58]], [[4y5a\|4y5a]], [[4y5b\|4y5b]], [[4y5c\|4y5c]], [[4y5e\|4y5e]], [[4y5k\|4y5k]], [[4y5l\|4y5l]], [[4y5m\|4y5m]], [[4y5n\|4y5n]], [[4y5p\|4y5p]], [[4yck\|4yck]], [[4yct\|4yct]], [[4ycy\|4ycy]], [[4yd3\|4yd3]], [[4yd4\|4yd4]], [[4yd5\|4yd5]], [[4yd6\|4yd6]], [[4yd7\|4yd7]], [[4y48\|4y48]], [[4y4j\|4y4j]], [[4y4g\|4y4g]], [[4y4d\|4y4d]], [[4y38\|4y38]], [[4y3y\|4y3y]], [[4y3j\|4y3j]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pgi\|3pgi]], [[4y35\|4y35]], [[4y36\|4y36]], [[4y37\|4y37]], [[4y39\|4y39]], [[4y3a\|4y3a]], [[4y3d\|4y3d]], [[4y3f\|4y3f]], [[4y3g\|4y3g]], [[4y3l\|4y3l]], [[4y3m\|4y3m]], [[4y3n\|4y3n]], [[4y3p\|4y3p]], [[4y3q\|4y3q]], [[4y3r\|4y3r]], [[4y3s\|4y3s]], [[4y3t\|4y3t]], [[4y3w\|4y3w]], [[4y3x\|4y3x]], [[4y3z\|4y3z]], [[4y41\|4y41]], [[4y43\|4y43]], [[4y44\|4y44]], [[4y45\|4y45]], [[4y47\|4y47]], [[4y4a\|4y4a]], [[4y4b\|4y4b]], [[4y4c\|4y4c]], [[4y4e\|4y4e]], [[4y4t\|4y4t]], [[4y4u\|4y4u]], [[4y4w\|4y4w]], [[4y4x\|4y4x]], [[4y4z\|4y4z]], [[4y50\|4y50]], [[4y51\|4y51]], [[4y53\|4y53]], [[4y54\|4y54]], [[4y56\|4y56]], [[4y57\|4y57]], [[4y58\|4y58]], [[4y5a\|4y5a]], [[4y5b\|4y5b]], [[4y5c\|4y5c]], [[4y5e\|4y5e]], [[4y5k\|4y5k]], [[4y5l\|4y5l]], [[4y5m\|4y5m]], [[4y5n\|4y5n]], [[4y5p\|4y5p]], [[4yck\|4yck]], [[4yct\|4yct]], [[4ycy\|4ycy]], [[4yd3\|4yd3]], [[4yd4\|4yd4]], [[4yd5\|4yd5]], [[4yd6\|4yd6]], [[4yd7\|4yd7]], [[4y48\|4y48]], [[4y4j\|4y4j]], [[4y4g\|4y4g]], [[4y4d\|4y4d]], [[4y38\|4y38]], [[4y3y\|4y3y]], [[4y3j\|4y3j]]</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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [http://pdbe.org/4y5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [http://www.ebi.ac.uk/pdbsum/4y5g 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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [http://pdbe.org/4y5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [http://www.ebi.ac.uk/pdbsum/4y5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y5g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 24:		Line 24:
	[[Category: Cryphonectria parasitica]]		[[Category: Cryphonectria parasitica]]
	[[Category: Endothiapepsin]]		[[Category: Endothiapepsin]]
		+	[[Category: Large Structures]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]

OCA at 15:11, 2 March 2016

OCA — Wed, 02 Mar 2016 15:11:52 GMT

←Older revision		Revision as of 15:11, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4y5g is ~~ON HOLD until Paper~~ Publication	+	==Endothiapepsin in complex with fragment 272==
		+	<StructureSection load='4y5g' size='340' side='right' caption='[[4y5g]], [[Resolution\|resolution]] 1.47Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4y5g]] 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=4Y5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y5G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=47U:N-(PYRIDIN-2-YL)-2-(1,3,5-TRIMETHYL-1H-PYRAZOL-4-YL)ACETAMIDE'>47U</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pgi\|3pgi]], [[4y35\|4y35]], [[4y36\|4y36]], [[4y37\|4y37]], [[4y39\|4y39]], [[4y3a\|4y3a]], [[4y3d\|4y3d]], [[4y3f\|4y3f]], [[4y3g\|4y3g]], [[4y3l\|4y3l]], [[4y3m\|4y3m]], [[4y3n\|4y3n]], [[4y3p\|4y3p]], [[4y3q\|4y3q]], [[4y3r\|4y3r]], [[4y3s\|4y3s]], [[4y3t\|4y3t]], [[4y3w\|4y3w]], [[4y3x\|4y3x]], [[4y3z\|4y3z]], [[4y41\|4y41]], [[4y43\|4y43]], [[4y44\|4y44]], [[4y45\|4y45]], [[4y47\|4y47]], [[4y4a\|4y4a]], [[4y4b\|4y4b]], [[4y4c\|4y4c]], [[4y4e\|4y4e]], [[4y4t\|4y4t]], [[4y4u\|4y4u]], [[4y4w\|4y4w]], [[4y4x\|4y4x]], [[4y4z\|4y4z]], [[4y50\|4y50]], [[4y51\|4y51]], [[4y53\|4y53]], [[4y54\|4y54]], [[4y56\|4y56]], [[4y57\|4y57]], [[4y58\|4y58]], [[4y5a\|4y5a]], [[4y5b\|4y5b]], [[4y5c\|4y5c]], [[4y5e\|4y5e]], [[4y5k\|4y5k]], [[4y5l\|4y5l]], [[4y5m\|4y5m]], [[4y5n\|4y5n]], [[4y5p\|4y5p]], [[4yck\|4yck]], [[4yct\|4yct]], [[4ycy\|4ycy]], [[4yd3\|4yd3]], [[4yd4\|4yd4]], [[4yd5\|4yd5]], [[4yd6\|4yd6]], [[4yd7\|4yd7]], [[4y48\|4y48]], [[4y4j\|4y4j]], [[4y4g\|4y4g]], [[4y4d\|4y4d]], [[4y38\|4y38]], [[4y3y\|4y3y]], [[4y3j\|4y3j]]</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=4y5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y5g OCA], [http://pdbe.org/4y5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y5g RCSB], [http://www.ebi.ac.uk/pdbsum/4y5g PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.

-	~~Authors: Wang, X~~., ~~Heine~~, A., Klebe, G.	+	A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes.,Koster H, Craan T, Brass S, Herhaus C, Zentgraf M, Neumann L, Heine A, Klebe G J Med Chem. 2011 Oct 25. PMID:21972967<ref>PMID:21972967</ref>

-	~~Description~~: ~~Endothiapepsin in complex with fragment 272~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 4y5g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cryphonectria parasitica]]
		+	[[Category: Endothiapepsin]]
	[[Category: Heine, A]]		[[Category: Heine, A]]
-	[[Category: Wang, X]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]
		+	[[Category: Wang, X]]
		+	[[Category: Aspartic protease]]
		+	[[Category: Fragment screening]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibition]]

OCA at 08:35, 9 December 2015

OCA — Wed, 09 Dec 2015 08:35:17 GMT

←Older revision		Revision as of 08:35, 9 December 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y5g is ON HOLD	+	The entry 4y5g is ON HOLD until Paper Publication

	Authors: Wang, X., Heine, A., Klebe, G.		Authors: Wang, X., Heine, A., Klebe, G.

OCA at 23:27, 30 November 2015

OCA — Mon, 30 Nov 2015 23:27:46 GMT

←Older revision		Revision as of 23:27, 30 November 2015
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	Description: Endothiapepsin in complex with fragment 272		Description: Endothiapepsin in complex with fragment 272
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Heine, A]]
	[[Category: Wang, X]]		[[Category: Wang, X]]
	[[Category: Klebe, G]]		[[Category: Klebe, G]]
-	[[Category: Heine, A]]

OCA at 23:22, 15 October 2015

OCA — Thu, 15 Oct 2015 23:22:22 GMT

←Older revision		Revision as of 23:22, 15 October 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y5g is ON HOLD ~~until Paper Publication~~	+	The entry 4y5g is ON HOLD

	Authors: Wang, X., Heine, A., Klebe, G.		Authors: Wang, X., Heine, A., Klebe, G.

OCA at 11:32, 8 July 2015

OCA — Wed, 08 Jul 2015 11:32:40 GMT

←Older revision		Revision as of 11:32, 8 July 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y5g is ON HOLD	+	The entry 4y5g is ON HOLD until Paper Publication

	Authors: Wang, X., Heine, A., Klebe, G.		Authors: Wang, X., Heine, A., Klebe, G.

OCA: Protected "4y5g" [edit=sysop:move=sysop]

OCA — Wed, 18 Feb 2015 12:03:02 GMT

Protected "4y5g" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:03, 18 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y5g is ON HOLD Authors: Wang, X., Heine, A., Klebe, G. Description: Endothiapepsin in complex with fragment 272 [[Category: Unreleased Structures]...

OCA — Wed, 18 Feb 2015 12:03:01 GMT

New page: '''Unreleased structure''' The entry 4y5g is ON HOLD Authors: Wang, X., Heine, A., Klebe, G. Description: Endothiapepsin in complex with fragment 272 [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 4y5g is ON HOLD

Authors: Wang, X., Heine, A., Klebe, G.

Description: Endothiapepsin in complex with fragment 272
[[Category: Unreleased Structures]]
[[Category: Wang, X]]
[[Category: Klebe, G]]
[[Category: Heine, A]]