7bdb - Revision history

OCA at 12:26, 1 February 2024

2024-02-01T12:26:09Z

←Older revision		Revision as of 12:26, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7bdb]] is a 1 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=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7bdb]] is a 1 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=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NW7:3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide'>NW7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.46Å</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NW7:3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide'>NW7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb 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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NOTUM_HUMAN NOTUM_HUMAN]] May deacetylate GlcNAc residues on cell surface glycans.	+	[https://www.uniprot.org/uniprot/NOTUM_HUMAN NOTUM_HUMAN] May deacetylate GlcNAc residues on cell surface glycans.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7bdb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7bdb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxylesterase 3D structures\|Carboxylesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:37, 8 September 2022

2022-09-08T04:37:52Z

←Older revision		Revision as of 04:37, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7bdb' size='340' side='right'caption='[[7bdb]], [[Resolution\|resolution]] 1.46Å' scene=''>		<StructureSection load='7bdb' size='340' side='right'caption='[[7bdb]], [[Resolution\|resolution]] 1.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bdb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bdb]] is a 1 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=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NW7:3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide'>NW7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NW7:3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide'>NW7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7b84\|7b84]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Wnt_protein]_O-palmitoleoyl-L-serine_hydrolase [Wnt protein] O-palmitoleoyl-L-serine hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.98 3.1.1.98] </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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb 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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/NOTUM_HUMAN NOTUM_HUMAN]] May deacetylate GlcNAc residues on cell surface glycans.	+	[[https://www.uniprot.org/uniprot/NOTUM_HUMAN NOTUM_HUMAN]] May deacetylate GlcNAc residues on cell surface glycans.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jones~~, E Y~~]]	+	[[Category: Jones EY]]
-	[[Category: Zhao, Y]]	+	[[Category: Zhao Y]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Notum inhibitor fragment screen~~]]	+

OCA at 18:12, 27 July 2022

2022-07-27T18:12:16Z

←Older revision		Revision as of 18:12, 27 July 2022
Line 1:		Line 1:

	==Notum Fragment 916==		==Notum Fragment 916==
-	<StructureSection load='7bdb' size='340' side='right'caption='[[7bdb]]' scene=''>	+	<StructureSection load='7bdb' size='340' side='right'caption='[[7bdb]], [[Resolution\|resolution]] 1.46Å' 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=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bdb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB 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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb 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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NW7:3-ethyl-5-methyl-N-(5-methyl-1,2-oxazol-3-yl)-1,2-oxazole-4-carboxamide'>NW7</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7b84\|7b84]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/[Wnt_protein]_O-palmitoleoyl-L-serine_hydrolase [Wnt protein] O-palmitoleoyl-L-serine hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.98 3.1.1.98] </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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/NOTUM_HUMAN NOTUM_HUMAN]] May deacetylate GlcNAc residues on cell surface glycans.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Wnt signaling suppressor Notum is a promising target for osteoporosis, Alzheimer's disease, and colorectal cancers. To develop novel Notum inhibitors, we used an X-ray crystallographic fragment screen with the Diamond-SGC Poised Library (DSPL) and identified 59 fragment hits from the analysis of 768 data sets. Fifty-eight of the hits were found bound at the enzyme catalytic pocket with potencies ranging from 0.5 to >1000 muM. Analysis of the fragments' diverse binding modes, enzymatic inhibitory activities, and chemical properties led to the selection of six hits for optimization, and five of these resulted in improved Notum inhibitory potencies. One hit, 1-phenyl-1,2,3-triazole 7, and its related cluster members, have shown promising lead-like properties. These became the focus of our fragment development activities, resulting in compound 7d with IC50 0.0067 muM. The large number of Notum fragment structures and their initial optimization provided an important basis for further Notum inhibitor development.
		+
		+	Structural Analysis and Development of Notum Fragment Screening Hits.,Zhao Y, Mahy W, Willis NJ, Woodward HL, Steadman D, Bayle ED, Atkinson BN, Sipthorp J, Vecchia L, Ruza RR, Harlos K, Jeganathan F, Constantinou S, Costa A, Kjaer S, Bictash M, Salinas PC, Whiting P, Vincent JP, Fish PV, Jones EY ACS Chem Neurosci. 2022 Jul 6;13(13):2060-2077. doi:, 10.1021/acschemneuro.2c00325. Epub 2022 Jun 22. PMID:35731924<ref>PMID:35731924</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bdb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jones EY]]	+	[[Category: Jones, E Y]]
-	[[Category: Zhao Y]]	+	[[Category: Zhao, Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Notum inhibitor fragment screen]]

OCA at 09:55, 12 January 2022

2022-01-12T09:55:12Z

←Older revision		Revision as of 09:55, 12 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7bdb ~~is ON HOLD until Paper Publication~~	+	==Notum Fragment 916==
-		+	<StructureSection load='7bdb' size='340' side='right'caption='[[7bdb]]' scene=''>
-	~~Authors~~: ~~Zhao~~, Y., ~~Jones~~, E.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BDB FirstGlance]. <br>
-	~~Description: Notum Fragment 916~~	+	</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=7bdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bdb OCA], [https://pdbe.org/7bdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bdb RCSB], [https://www.ebi.ac.uk/pdbsum/7bdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bdb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Zhao, Y~~]]	+	__TOC__
-	[[Category: ~~Jones, E.~~Y]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jones EY]]
		+	[[Category: Zhao Y]]

OCA at 06:36, 20 January 2021

2021-01-20T06:36:52Z

←Older revision		Revision as of 06:36, 20 January 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7bdb is ON HOLD	+	The entry 7bdb is ON HOLD until Paper Publication

	Authors: Zhao, Y., Jones, E.Y.		Authors: Zhao, Y., Jones, E.Y.

OCA: Protected "7bdb" [edit=sysop:move=sysop]

2020-12-30T05:17:29Z

Protected "7bdb" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:17, 30 December 2020

OCA: New page: '''Unreleased structure''' The entry 7bdb is ON HOLD Authors: Zhao, Y., Jones, E.Y. Description: Notum Fragment 916 Category: Unreleased Structures Category: Zhao, Y [[Category...

2020-12-30T05:17:28Z

New page: '''Unreleased structure''' The entry 7bdb is ON HOLD Authors: Zhao, Y., Jones, E.Y. Description: Notum Fragment 916 Category: Unreleased Structures Category: Zhao, Y [[Category...

New page

'''Unreleased structure'''

The entry 7bdb is ON HOLD

Authors: Zhao, Y., Jones, E.Y.

Description: Notum Fragment 916
[[Category: Unreleased Structures]]
[[Category: Zhao, Y]]
[[Category: Jones, E.Y]]