5f03 - Revision history

OCA at 07:22, 1 May 2024

OCA — Wed, 01 May 2024 07:22:34 GMT

←Older revision		Revision as of 07:22, 1 May 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TRYB1_HUMAN TRYB1_HUMAN] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity).		[https://www.uniprot.org/uniprot/TRYB1_HUMAN TRYB1_HUMAN] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity).
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.
-
-	A Real-World Perspective on Molecular Design.,Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Korner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M J Med Chem. 2016 Feb 24. PMID:26878596<ref>PMID:26878596</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5f03" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Tryptase\|Tryptase]]		*[[Tryptase\|Tryptase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:37, 12 July 2023

OCA — Wed, 12 Jul 2023 08:37:35 GMT

←Older revision		Revision as of 08:37, 12 July 2023
Line 3:		Line 3:
	<StructureSection load='5f03' size='340' side='right'caption='[[5f03]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5f03' size='340' side='right'caption='[[5f03]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f03]] is a 2 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=5F03 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F03 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f03]] is a 2 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=5F03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F03 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5TA:(5~{S})-5-[[3-(AMINOMETHYL)PHENOXY]METHYL]-3-[3-[2-(2-CHLORANYLPYRIDIN-3-YL)ETHYNYL]PHENYL]-1,3-OXAZOLIDIN-2-ONE'>5TA</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]] 1.94Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TPSB2, TPS2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5TA:(5~{S})-5-[[3-(AMINOMETHYL)PHENOXY]METHYL]-3-[3-[2-(2-CHLORANYLPYRIDIN-3-YL)ETHYNYL]PHENYL]-1,3-OXAZOLIDIN-2-ONE'>5TA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptase Tryptase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.59 3.4.21.59] </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=5f03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f03 OCA], [https://pdbe.org/5f03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f03 RCSB], [https://www.ebi.ac.uk/pdbsum/5f03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f03 ProSAT]</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=5f03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f03 OCA], [~~http~~://pdbe.org/5f03 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f03 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f03 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f03 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~TRYB2_HUMAN TRYB2_HUMAN]~~] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type~~. Has an immunoprotective role during bacterial infection. Required to efficiently combat K.pneumoniae infection~~ (By similarity).	+	[https://www.uniprot.org/uniprot/TRYB1_HUMAN TRYB1_HUMAN] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Tryptase]]~~	+	[[Category: Banner D]]
-	[[Category: Banner, D]]	+	[[Category: Benz J]]
-	[[Category: Benz, J]]	+	[[Category: Joseph C]]
-	[[Category: Joseph, C]]	+	[[Category: Kuglstatter A]]
-	[[Category: Kuglstatter, A]]	+
-	~~[[Category: Human tryptase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Serine proteinase~~]]	+

OCA at 08:11, 20 March 2019

OCA — Wed, 20 Mar 2019 08:11:37 GMT

←Older revision		Revision as of 08:11, 20 March 2019
Line 1:		Line 1:

	==TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid==		==TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid==
-	<StructureSection load='5f03' size='340' side='right' caption='[[5f03]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='5f03' size='340' side='right'caption='[[5f03]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f03]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F03 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f03]] is a 2 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=5F03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F03 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5TA:(5~{S})-5-[[3-(AMINOMETHYL)PHENOXY]METHYL]-3-[3-[2-(2-CHLORANYLPYRIDIN-3-YL)ETHYNYL]PHENYL]-1,3-OXAZOLIDIN-2-ONE'>5TA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5TA:(5~{S})-5-[[3-(AMINOMETHYL)PHENOXY]METHYL]-3-[3-[2-(2-CHLORANYLPYRIDIN-3-YL)ETHYNYL]PHENYL]-1,3-OXAZOLIDIN-2-ONE'>5TA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TPSB2, TPS2 ([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/Tryptase Tryptase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.59 3.4.21.59] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptase Tryptase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.59 3.4.21.59] </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=5f03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f03 OCA], [http://pdbe.org/5f03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f03 RCSB], [http://www.ebi.ac.uk/pdbsum/5f03 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=5f03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f03 OCA], [http://pdbe.org/5f03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f03 RCSB], [http://www.ebi.ac.uk/pdbsum/5f03 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f03 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~TRYB1_HUMAN TRYB1_HUMAN~~]] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity).	+	[[http://www.uniprot.org/uniprot/TRYB2_HUMAN TRYB2_HUMAN]] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type. Has an immunoprotective role during bacterial infection. Required to efficiently combat K.pneumoniae infection (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5f03" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5f03" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tryptase\|Tryptase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Tryptase]]		[[Category: Tryptase]]
	[[Category: Banner, D]]		[[Category: Banner, D]]

OCA at 18:03, 26 February 2016

OCA — Fri, 26 Feb 2016 18:03:47 GMT

←Older revision		Revision as of 18:03, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5f03 is ~~ON HOLD until Paper~~ Publication	+	==TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid==
		+	<StructureSection load='5f03' size='340' side='right' caption='[[5f03]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5f03]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F03 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5TA:(5~{S})-5-[[3-(AMINOMETHYL)PHENOXY]METHYL]-3-[3-[2-(2-CHLORANYLPYRIDIN-3-YL)ETHYNYL]PHENYL]-1,3-OXAZOLIDIN-2-ONE'>5TA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptase Tryptase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.59 3.4.21.59] </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=5f03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f03 OCA], [http://pdbe.org/5f03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f03 RCSB], [http://www.ebi.ac.uk/pdbsum/5f03 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TRYB1_HUMAN TRYB1_HUMAN]] Tryptase is the major neutral protease present in mast cells and is secreted upon the coupled activation-degranulation response of this cell type (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

-	~~Authors: Banner, D~~., ~~Benz~~, J., ~~Joseph~~, C., ~~Kuglstatter~~, A.	+	A Real-World Perspective on Molecular Design.,Kuhn B, Guba W, Hert J, Banner D, Bissantz C, Ceccarelli S, Haap W, Korner M, Kuglstatter A, Lerner C, Mattei P, Neidhart W, Pinard E, Rudolph MG, Schulz-Gasch T, Woltering T, Stahl M J Med Chem. 2016 Feb 24. PMID:26878596<ref>PMID:26878596</ref>

-	~~Description: TRYPTASE B2 IN COMPLEX WITH 5~~-~~(3-Aminomethyl-phenoxymethyl)-3~~-[~~3-(2-chloro-pyridin-3-ylethynyl)-phenyl~~]~~-oxazolidin-2-one; compound with trifluoro-acetic acid~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5f03" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tryptase]]
		+	[[Category: Banner, D]]
		+	[[Category: Benz, J]]
	[[Category: Joseph, C]]		[[Category: Joseph, C]]
	[[Category: Kuglstatter, A]]		[[Category: Kuglstatter, A]]
-	[[Category: ~~Benz, J~~]]	+	[[Category: Human tryptase]]
-	[[Category: ~~Banner, D~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Serine proteinase]]

OCA at 12:25, 9 December 2015

OCA — Wed, 09 Dec 2015 12:25:06 GMT

←Older revision		Revision as of 12:25, 9 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f03 is ON HOLD	+	The entry 5f03 is ON HOLD until Paper Publication

	Authors: Banner, D., Benz, J., Joseph, C., Kuglstatter, A.		Authors: Banner, D., Benz, J., Joseph, C., Kuglstatter, A.

OCA: Protected "5f03" [edit=sysop:move=sysop]

OCA — Wed, 02 Dec 2015 15:14:10 GMT

Protected "5f03" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:14, 2 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f03 is ON HOLD Authors: Banner, D., Benz, J., Joseph, C., Kuglstatter, A. Description: TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)...

OCA — Wed, 02 Dec 2015 15:14:09 GMT

New page: '''Unreleased structure''' The entry 5f03 is ON HOLD Authors: Banner, D., Benz, J., Joseph, C., Kuglstatter, A. Description: TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)...

New page

'''Unreleased structure'''

The entry 5f03 is ON HOLD

Authors: Banner, D., Benz, J., Joseph, C., Kuglstatter, A.

Description: TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid
[[Category: Unreleased Structures]]
[[Category: Joseph, C]]
[[Category: Kuglstatter, A]]
[[Category: Benz, J]]
[[Category: Banner, D]]