5qdc - Revision history

OCA at 08:51, 7 February 2024

OCA — Wed, 07 Feb 2024 08:51:54 GMT

←Older revision		Revision as of 08:51, 7 February 2024
Line 1:		Line 1:

	==Crystal structure of BACE complex with BMC019 hydrolyzed==		==Crystal structure of BACE complex with BMC019 hydrolyzed==
-	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]]' scene=''>	+	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]], [[Resolution\|resolution]] 2.10Å' 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=5QDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5qdc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>
-	</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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [https://pdbe.org/5qdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [https://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E77:(4S)-4-[(1R)-1,2-dihydroxyethyl]-N,N-dimethyl-2-oxo-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaene-19-carboxamide'>E77</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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [https://pdbe.org/5qdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [https://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BACE1_HUMAN BACE1_HUMAN] Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase.<ref>PMID:10677483</ref> <ref>PMID:20354142</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rondeau, JM, Shao, C, Yang, H~~, Burley, SK~~]]	+	[[Category: Burley SK]]
		+	[[Category: Rondeau JM]]
		+	[[Category: Shao C]]
		+	[[Category: Yang H]]

OCA at 14:59, 8 June 2021

OCA — Tue, 08 Jun 2021 14:59:06 GMT

←Older revision		Revision as of 14:59, 8 June 2021
Line 1:		Line 1:

	==Crystal structure of BACE complex with BMC019 hydrolyzed==		==Crystal structure of BACE complex with BMC019 hydrolyzed==
-	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]]~~, [[Resolution\|resolution]] 2.10Å~~' scene=''>	+	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[5qdc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QDC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E77:(4S)-4-[(1R)-1,2-dihydroxyethyl]-N,N-dimethyl-2-oxo-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaene-19-carboxamide'>E77</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [https://pdbe.org/5qdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [https://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACE1, BACE, KIAA1149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Memapsin_2 Memapsin 2], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.46 3.4.23.46] </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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [~~http~~://pdbe.org/5qdc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/BACE1_HUMAN BACE1_HUMAN]] Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase.<ref>PMID:10677483</ref> <ref>PMID:20354142</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. We provide an analysis of the results and discuss insights into determined best practice methods.
-
-	D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.,Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK J Comput Aided Mol Des. 2020 Feb;34(2):99-119. doi: 10.1007/s10822-020-00289-y., Epub 2020 Jan 23. PMID:31974851<ref>PMID:31974851</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5qdc" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Memapsin 2]]~~	+	[[Category: Rondeau, JM, Shao, C, Yang, H, Burley, SK]]
-	~~[[Category: Burley, S K]]~~	+
-	[[Category: Rondeau, ~~J M]]~~	+
-	~~[[Category:~~ Shao, C]]	+
-	~~[[Category:~~ Yang, H]]	+
-	~~[[Category: Bace]]~~	+
-	~~[[Category: D3r]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydroloase]]~~	+
-	~~[[Category: Ligand docking~~]]	+

OCA at 06:52, 30 December 2020

OCA — Wed, 30 Dec 2020 06:52:37 GMT

←Older revision		Revision as of 06:52, 30 December 2020
Line 1:		Line 1:

	==Crystal structure of BACE complex with BMC019 hydrolyzed==		==Crystal structure of BACE complex with BMC019 hydrolyzed==
-	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]]' scene=''>	+	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]], [[Resolution\|resolution]] 2.10Å' 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=5QDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5qdc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5QDC 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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [http://pdbe.org/5qdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [http://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E77:(4S)-4-[(1R)-1,2-dihydroxyethyl]-N,N-dimethyl-2-oxo-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaene-19-carboxamide'>E77</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BACE1, BACE, KIAA1149 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Memapsin_2 Memapsin 2], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.46 3.4.23.46] </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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [http://pdbe.org/5qdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [http://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACE1_HUMAN BACE1_HUMAN]] Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase.<ref>PMID:10677483</ref> <ref>PMID:20354142</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. We provide an analysis of the results and discuss insights into determined best practice methods.
		+
		+	D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.,Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK J Comput Aided Mol Des. 2020 Feb;34(2):99-119. doi: 10.1007/s10822-020-00289-y., Epub 2020 Jan 23. PMID:31974851<ref>PMID:31974851</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5qdc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rondeau, ~~JM,~~ Shao, C, Yang, H~~, Burley, SK~~]]	+	[[Category: Memapsin 2]]
		+	[[Category: Burley, S K]]
		+	[[Category: Rondeau, J M]]
		+	[[Category: Shao, C]]
		+	[[Category: Yang, H]]
		+	[[Category: Bace]]
		+	[[Category: D3r]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydroloase]]
		+	[[Category: Ligand docking]]

OCA at 06:21, 3 June 2020

OCA — Wed, 03 Jun 2020 06:21:42 GMT

←Older revision		Revision as of 06:21, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5qdc is ON HOLD until Paper Publication~~	+	==Crystal structure of BACE complex with BMC019 hydrolyzed==
-		+	<StructureSection load='5qdc' size='340' side='right'caption='[[5qdc]]' scene=''>
-	~~Authors: Rondeau, J.M., Shao, C., Yang, H., Burley, S.K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5QDC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5QDC FirstGlance]. <br>
-	~~Description:~~ Crystal structure of BACE complex with BMC019 hydrolyzed	+	</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=5qdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5qdc OCA], [http://pdbe.org/5qdc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5qdc RCSB], [http://www.ebi.ac.uk/pdbsum/5qdc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5qdc ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Burley, S~~.K]]	+	__TOC__
-	[[~~Category~~: ~~Rondeau~~, J.M]]	+	</StructureSection>
-	[[Category: ~~Yang, H~~]]	+	[[Category: Large Structures]]
-	[[Category: Shao, C]]	+	[[Category: Rondeau, JM, Shao, C, Yang, H, Burley, SK]]

OCA at 04:26, 27 May 2020

OCA — Wed, 27 May 2020 04:26:50 GMT

←Older revision		Revision as of 04:26, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5qdc is ON HOLD	+	The entry 5qdc is ON HOLD until Paper Publication

-	Authors: Rondeau, J.M., ~~Yang~~, H., ~~Shao~~, C., Burley, S.	+	Authors: Rondeau, J.M., Shao, C., Yang, H., Burley, S.K.

-	Description: Crystal ~~Structures~~ of ~~Beta-Secretase 1~~ with ~~Bound Ligand~~	+	Description: Crystal structure of BACE complex with BMC019 hydrolyzed
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Burley, S.K]]
		+	[[Category: Rondeau, J.M]]
	[[Category: Yang, H]]		[[Category: Yang, H]]
	[[Category: Shao, C]]		[[Category: Shao, C]]
-	[[Category: Burley, S]]
-	[[Category: Rondeau, J.M]]

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

OCA — Wed, 13 Dec 2017 05:44:02 GMT

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

←Older revision

Revision as of 05:44, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 5qdc is ON HOLD Authors: Rondeau, J.M., Yang, H., Shao, C., Burley, S. Description: Crystal Structures of Beta-Secretase 1 with Bound Ligand [[Cate...

OCA — Wed, 13 Dec 2017 05:44:00 GMT

New page: '''Unreleased structure''' The entry 5qdc is ON HOLD Authors: Rondeau, J.M., Yang, H., Shao, C., Burley, S. Description: Crystal Structures of Beta-Secretase 1 with Bound Ligand [[Cate...

New page

'''Unreleased structure'''

The entry 5qdc is ON HOLD

Authors: Rondeau, J.M., Yang, H., Shao, C., Burley, S.

Description: Crystal Structures of Beta-Secretase 1 with Bound Ligand
[[Category: Unreleased Structures]]
[[Category: Yang, H]]
[[Category: Shao, C]]
[[Category: Burley, S]]
[[Category: Rondeau, J.M]]