7z2i - Revision history

OCA at 07:55, 1 May 2024

OCA — Wed, 01 May 2024 07:55:02 GMT

←Older revision		Revision as of 07:55, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7z2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>		<table><tr><td colspan='2'>[[7z2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</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]] 1.09Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i 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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]]	+	[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]

	==See Also==		==See Also==

OCA at 05:34, 8 September 2022

OCA — Thu, 08 Sep 2022 05:34:31 GMT

←Older revision		Revision as of 05:34, 8 September 2022
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[7z2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>		<table><tr><td colspan='2'>[[7z2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</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;'>[[7z25\|7z25]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i 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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[[https://www.uniprot.org/uniprot/TRY1_BOVIN TRY1_BOVIN]]
-	Ligand-based (19) F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental (19) F NMR chemical shifts. Here, we introduce a complementary knowledge-based (19) F NMR screening approach, named (19) Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted (19) F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift, for (19) F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.	+
-		+
-	Efficient Screening of Target-Specific Selected Compounds in Mixtures by (19) F NMR Binding Assay with Predicted (19) F NMR Chemical Shifts.,Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y ChemMedChem. 2022 Apr 27:~~e202200163. doi: 10.1002~~/~~cmdc.202200163. PMID:35475323<ref>PMID:35475323<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7z2i" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Trypsin 3D structures\|Trypsin 3D structures]]		*[[Trypsin 3D structures\|Trypsin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Trypsin]]~~	+	[[Category: Dalvit C]]
-	[[Category: Dalvit, C]]	+	[[Category: Schiering N]]
-	[[Category: Schiering, N]]	+	[[Category: Vulpetti A]]
-	[[Category: Vulpetti, A]]	+
-	~~[[Category: Fluorine containing small molecule inhibitor]]~~	+
-	~~[[Category: Fragment complex]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 05:29, 13 July 2022

OCA — Wed, 13 Jul 2022 05:29:37 GMT

←Older revision		Revision as of 05:29, 13 July 2022
Line 1:		Line 1:

	==TRYPSIN (BOVINE) COMPLEXED WITH compound 4==		==TRYPSIN (BOVINE) COMPLEXED WITH compound 4==
-	<StructureSection load='7z2i' size='340' side='right'caption='[[7z2i]]' scene=''>	+	<StructureSection load='7z2i' size='340' side='right'caption='[[7z2i]], [[Resolution\|resolution]] 1.09Å' 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=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I 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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=I9O:5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine'>I9O</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;'>[[7z25\|7z25]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Trypsin Trypsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.4 3.4.21.4] </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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ligand-based (19) F NMR screening is a highly effective and well-established hit-finding approach. The high sensitivity to protein binding makes it particularly suitable for fragment screening. Different criteria can be considered for generating fluorinated fragment libraries. One common strategy is to assemble a large, diverse, well-designed and characterized fragment library which is screened in mixtures, generated based on experimental (19) F NMR chemical shifts. Here, we introduce a complementary knowledge-based (19) F NMR screening approach, named (19) Focused screening, enabling the efficient screening of putative active molecules selected by computational hit finding methodologies, in mixtures assembled and on-the-fly deconvoluted based on predicted (19) F NMR chemical shifts. In this study, we developed a novel approach, named LEFshift, for (19) F NMR chemical shift prediction using rooted topological fluorine torsion fingerprints in combination with a random forest machine learning method. A demonstration of this approach to a real test case is reported.
		+
		+	Efficient Screening of Target-Specific Selected Compounds in Mixtures by (19) F NMR Binding Assay with Predicted (19) F NMR Chemical Shifts.,Vulpetti A, Lingel A, Dalvit C, Schiering N, Oberer L, Henry C, Lu Y ChemMedChem. 2022 Apr 27:e202200163. doi: 10.1002/cmdc.202200163. PMID:35475323<ref>PMID:35475323</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z2i" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Trypsin 3D structures\|Trypsin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dalvit C]]	+	[[Category: Trypsin]]
-	[[Category: Schiering N]]	+	[[Category: Dalvit, C]]
-	[[Category: Vulpetti A]]	+	[[Category: Schiering, N]]
		+	[[Category: Vulpetti, A]]
		+	[[Category: Fluorine containing small molecule inhibitor]]
		+	[[Category: Fragment complex]]
		+	[[Category: Hydrolase]]

OCA at 08:01, 25 May 2022

OCA — Wed, 25 May 2022 08:01:07 GMT

←Older revision		Revision as of 08:01, 25 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7z2i is ~~ON HOLD until Paper Publication~~	+	==TRYPSIN (BOVINE) COMPLEXED WITH compound 4==
-		+	<StructureSection load='7z2i' size='340' side='right'caption='[[7z2i]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Z2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z2I FirstGlance]. <br>
-	~~Description~~:	+	</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=7z2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z2i OCA], [https://pdbe.org/7z2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z2i RCSB], [https://www.ebi.ac.uk/pdbsum/7z2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z2i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Dalvit C]]
		+	[[Category: Schiering N]]
		+	[[Category: Vulpetti A]]

OCA at 09:19, 6 April 2022

OCA — Wed, 06 Apr 2022 09:19:09 GMT

←Older revision		Revision as of 09:19, 6 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z2i is ON HOLD	+	The entry 7z2i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7z2i" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2022 05:10:52 GMT

Protected "7z2i" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:10, 9 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z2i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 Mar 2022 05:10:51 GMT

New page: '''Unreleased structure''' The entry 7z2i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7z2i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]