6fil - Revision history

OCA at 07:33, 1 May 2024

OCA — Wed, 01 May 2024 07:33:00 GMT

←Older revision		Revision as of 07:33, 1 May 2024
Line 3:		Line 3:
	<StructureSection load='6fil' size='340' side='right'caption='[[6fil]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='6fil' size='340' side='right'caption='[[6fil]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6fil]] is a 1 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=6FIL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6FIL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6fil]] 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=6FIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FIL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D6W:2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide'>D6W</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 1.73Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fer\|6fer]], [[6few\|6few]], [[6fex\|6fex]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D6W:2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide'>D6W</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6fil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fil OCA], [https://pdbe.org/6fil PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fil RCSB], [https://www.ebi.ac.uk/pdbsum/6fil PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fil 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/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=6fil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fil OCA], [~~http~~://pdbe.org/6fil PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6fil RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6fil PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6fil ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/DDR1_HUMAN DDR1_HUMAN]
-	The importance of DDR1 in renal fibrosis has been shown via gene knockout and use of antisense oligonucleotides; however, these techniques act via a reduction of DDR1 protein while we prove the therapeutic potential of inhibiting DDR1 phosphorylation with a small molecule. To date, efforts to generate a selective small-molecule to specifically modulate the activity of DDR1 in an in vivo model have been unsuccessful. We performed parallel DNA encoded library screens against DDR1 and DDR2, and discovered a chemical series that is highly selective for DDR1 over DDR2. Structure-guided optimization efforts yielded the potent DDR1 inhibitor 2.45, which possesses excellent kinome selectivity (including 64-fold selectivity over DDR2 in a biochemical assay), a clean in vitro safety profile, and favorable pharmacokinetic and physicochemical properties. As desired, compound 2.45 modulates DDR1 phosphorylation in vitro as well as prevents collagen-induced activation of renal epithelial cells expressing DDR1. Compound 2.45 preserves renal function and reduces tissue damage in Col4a3-/- mice (the preclinical mouse model of Alport syndrome) when employing a therapeutic dosing regime, indicating the real therapeutic value of selectively inhibiting DDR1 phosphorylation in vivo. Our results may have wider significance as Col4a3-/- mice also represent a model for chronic kidney disease, a disease which affects 10% of the global population.	+
-		+
-	DNA-encoded library-derived DDR1 inhibitor prevents fibrosis and renal function loss in a genetic mouse model of Alport syndrome.,Richter H, Satz AL, Bedoucha M, Buettelmann B, Petersen AC, Harmeier A, Hermosilla R, Hochstrasser R, Burger D, Gsell B, Gasser R, Huber S, Hug MN, Kocer B, Kuhn B, Ritter M, Rudolph MG, Weibel F, Molina-David J, Kim JJ, Santos JV, Stihle M, Georges GJ, Bonfil RD, Fridman R, Uhles S, Moll S, Faul C, Fornoni A, Prunotto M ACS Chem Biol. 2018 Nov 19. doi: ~~10.1021~~/~~acschembio.8b00866. PMID:30452219<ref>PMID:30452219<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6fil" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Epithelial discoidin domain-containing receptor\|Epithelial discoidin domain-containing receptor]]		*[[Epithelial discoidin domain-containing receptor\|Epithelial discoidin domain-containing receptor]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Receptor protein-tyrosine kinase]]~~	+	[[Category: Benz J]]
-	[[Category: Benz, J]]	+	[[Category: Kuhn B]]
-	[[Category: Kuhn, B]]	+	[[Category: Richter H]]
-	[[Category: Richter, H]]	+	[[Category: Rudolph MG]]
-	[[Category: Rudolph~~, M G~~]]	+	[[Category: Stihle M]]
-	[[Category: Stihle, M]]	+
-	~~[[Category: Collagen]]~~	+
-	~~[[Category: Discoidin domain]]~~	+
-	~~[[Category: Receptor tyrosine kinase]]~~	+
-	~~[[Category: Rtk]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:02, 27 March 2019

OCA — Wed, 27 Mar 2019 07:02:02 GMT

←Older revision		Revision as of 07:02, 27 March 2019
Line 1:		Line 1:

	==DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.730A, P212121, Rfree=24.5%==		==DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.730A, P212121, Rfree=24.5%==
-	<StructureSection load='6fil' size='340' side='right' caption='[[6fil]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='6fil' size='340' side='right'caption='[[6fil]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6fil]] is a 1 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=6FIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FIL FirstGlance]. <br>		<table><tr><td colspan='2'>[[6fil]] is a 1 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=6FIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FIL FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6fil" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6fil" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Epithelial discoidin domain-containing receptor\|Epithelial discoidin domain-containing receptor]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Receptor protein-tyrosine kinase]]		[[Category: Receptor protein-tyrosine kinase]]
	[[Category: Benz, J]]		[[Category: Benz, J]]

OCA at 20:30, 2 December 2018

OCA — Sun, 02 Dec 2018 20:30:24 GMT

←Older revision		Revision as of 20:30, 2 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6fil is ~~ON HOLD~~	+	==DDR1, 2-[8-(1H-indazole-5-carbonyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-N-methylacetamide, 1.730A, P212121, Rfree=24.5%==
		+	<StructureSection load='6fil' size='340' side='right' caption='[[6fil]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6fil]] is a 1 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=6FIL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FIL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D6W:2-[8-(2~{H}-indazol-5-ylcarbonyl)-4-oxidanylidene-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl]-~{N}-methyl-ethanamide'>D6W</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6fer\|6fer]], [[6few\|6few]], [[6fex\|6fex]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE ([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/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=6fil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fil OCA], [http://pdbe.org/6fil PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fil RCSB], [http://www.ebi.ac.uk/pdbsum/6fil PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fil ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The importance of DDR1 in renal fibrosis has been shown via gene knockout and use of antisense oligonucleotides; however, these techniques act via a reduction of DDR1 protein while we prove the therapeutic potential of inhibiting DDR1 phosphorylation with a small molecule. To date, efforts to generate a selective small-molecule to specifically modulate the activity of DDR1 in an in vivo model have been unsuccessful. We performed parallel DNA encoded library screens against DDR1 and DDR2, and discovered a chemical series that is highly selective for DDR1 over DDR2. Structure-guided optimization efforts yielded the potent DDR1 inhibitor 2.45, which possesses excellent kinome selectivity (including 64-fold selectivity over DDR2 in a biochemical assay), a clean in vitro safety profile, and favorable pharmacokinetic and physicochemical properties. As desired, compound 2.45 modulates DDR1 phosphorylation in vitro as well as prevents collagen-induced activation of renal epithelial cells expressing DDR1. Compound 2.45 preserves renal function and reduces tissue damage in Col4a3-/- mice (the preclinical mouse model of Alport syndrome) when employing a therapeutic dosing regime, indicating the real therapeutic value of selectively inhibiting DDR1 phosphorylation in vivo. Our results may have wider significance as Col4a3-/- mice also represent a model for chronic kidney disease, a disease which affects 10% of the global population.

-	~~Authors~~:	+	DNA-encoded library-derived DDR1 inhibitor prevents fibrosis and renal function loss in a genetic mouse model of Alport syndrome.,Richter H, Satz AL, Bedoucha M, Buettelmann B, Petersen AC, Harmeier A, Hermosilla R, Hochstrasser R, Burger D, Gsell B, Gasser R, Huber S, Hug MN, Kocer B, Kuhn B, Ritter M, Rudolph MG, Weibel F, Molina-David J, Kim JJ, Santos JV, Stihle M, Georges GJ, Bonfil RD, Fridman R, Uhles S, Moll S, Faul C, Fornoni A, Prunotto M ACS Chem Biol. 2018 Nov 19. doi: 10.1021/acschembio.8b00866. PMID:30452219<ref>PMID:30452219</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6fil" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Receptor protein-tyrosine kinase]]
		+	[[Category: Benz, J]]
		+	[[Category: Kuhn, B]]
		+	[[Category: Richter, H]]
		+	[[Category: Rudolph, M G]]
		+	[[Category: Stihle, M]]
		+	[[Category: Collagen]]
		+	[[Category: Discoidin domain]]
		+	[[Category: Receptor tyrosine kinase]]
		+	[[Category: Rtk]]
		+	[[Category: Transferase]]

OCA: Protected "6fil" [edit=sysop:move=sysop]

OCA — Wed, 24 Jan 2018 17:30:16 GMT

Protected "6fil" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:30, 24 January 2018

OCA: New page: '''Unreleased structure''' The entry 6fil is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Jan 2018 17:30:15 GMT

New page: '''Unreleased structure''' The entry 6fil is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6fil is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]