7dtz - Revision history

OCA at 16:39, 29 November 2023

2023-11-29T16:39:32Z

←Older revision		Revision as of 16:39, 29 November 2023
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	<StructureSection load='7dtz' size='340' side='right'caption='[[7dtz]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='7dtz' size='340' side='right'caption='[[7dtz]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dtz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DTZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dtz]] 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=7DTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DTZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HHL:N-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide'>HHL</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]] 2.01Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FGFR4, JTK2, TKF ([https://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=HHL:N-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide'>HHL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7dtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dtz OCA], [https://pdbe.org/7dtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dtz RCSB], [https://www.ebi.ac.uk/pdbsum/7dtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dtz 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=7dtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dtz OCA], [https://pdbe.org/7dtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dtz RCSB], [https://www.ebi.ac.uk/pdbsum/7dtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dtz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FGFR4_HUMAN FGFR4_HUMAN]] Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays a role in the regulation of cell proliferation, differentiation and migration, and in regulation of lipid metabolism, bile acid biosynthesis, glucose uptake, vitamin D metabolism and phosphate homeostasis. Required for normal down-regulation of the expression of CYP7A1, the rate-limiting enzyme in bile acid synthesis, in response to FGF19. Phosphorylates PLCG1 and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Promotes SRC-dependent phosphorylation of the matrix protease MMP14 and its lysosomal degradation. FGFR4 signaling is down-regulated by receptor internalization and degradation; MMP14 promotes internalization and degradation of FGFR4. Mutations that lead to constitutive kinase activation or impair normal FGFR4 inactivation lead to aberrant signaling.<ref>PMID:7680645</ref> <ref>PMID:7518429</ref> <ref>PMID:8663044</ref> <ref>PMID:11433297</ref> <ref>PMID:16597617</ref> <ref>PMID:17623664</ref> <ref>PMID:17311277</ref> <ref>PMID:18480409</ref> <ref>PMID:18670643</ref> <ref>PMID:20683963</ref> <ref>PMID:20018895</ref> <ref>PMID:20798051</ref> <ref>PMID:21653700</ref> <ref>PMID:20876804</ref>	+	[https://www.uniprot.org/uniprot/FGFR4_HUMAN FGFR4_HUMAN] Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays a role in the regulation of cell proliferation, differentiation and migration, and in regulation of lipid metabolism, bile acid biosynthesis, glucose uptake, vitamin D metabolism and phosphate homeostasis. Required for normal down-regulation of the expression of CYP7A1, the rate-limiting enzyme in bile acid synthesis, in response to FGF19. Phosphorylates PLCG1 and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Promotes SRC-dependent phosphorylation of the matrix protease MMP14 and its lysosomal degradation. FGFR4 signaling is down-regulated by receptor internalization and degradation; MMP14 promotes internalization and degradation of FGFR4. Mutations that lead to constitutive kinase activation or impair normal FGFR4 inactivation lead to aberrant signaling.<ref>PMID:7680645</ref> <ref>PMID:7518429</ref> <ref>PMID:8663044</ref> <ref>PMID:11433297</ref> <ref>PMID:16597617</ref> <ref>PMID:17623664</ref> <ref>PMID:17311277</ref> <ref>PMID:18480409</ref> <ref>PMID:18670643</ref> <ref>PMID:20683963</ref> <ref>PMID:20018895</ref> <ref>PMID:20798051</ref> <ref>PMID:21653700</ref> <ref>PMID:20876804</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7dtz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dtz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Fibroblast growth factor receptor 3D receptor\|Fibroblast growth factor receptor 3D receptor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Receptor protein-tyrosine kinase]]~~	+	[[Category: Chen XJ]]
-	[[Category: Chen~~, X J~~]]	+	[[Category: Chen YH]]
-	[[Category: Chen~~, Y H~~]]	+	[[Category: Dai SY]]
-	[[Category: Dai~~, S Y]]~~	+
-	~~[[Category: Covalent]]~~	+
-	~~[[Category: Crystal]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:32, 28 April 2021

2021-04-28T05:32:27Z

←Older revision		Revision as of 05:32, 28 April 2021
Line 1:		Line 1:

	==FGFR4 complex with a covalent inhibitor==		==FGFR4 complex with a covalent inhibitor==
-	<StructureSection load='7dtz' size='340' side='right'caption='[[7dtz]]' scene=''>	+	<StructureSection load='7dtz' size='340' side='right'caption='[[7dtz]], [[Resolution\|resolution]] 2.01Å' 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=7DTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DTZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dtz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DTZ 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=7dtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dtz OCA], [https://pdbe.org/7dtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dtz RCSB], [https://www.ebi.ac.uk/pdbsum/7dtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dtz 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=HHL:N-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide'>HHL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">FGFR4, JTK2, TKF ([https://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'>[https://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=7dtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dtz OCA], [https://pdbe.org/7dtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dtz RCSB], [https://www.ebi.ac.uk/pdbsum/7dtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dtz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/FGFR4_HUMAN FGFR4_HUMAN]] Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays a role in the regulation of cell proliferation, differentiation and migration, and in regulation of lipid metabolism, bile acid biosynthesis, glucose uptake, vitamin D metabolism and phosphate homeostasis. Required for normal down-regulation of the expression of CYP7A1, the rate-limiting enzyme in bile acid synthesis, in response to FGF19. Phosphorylates PLCG1 and FRS2. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. Promotes SRC-dependent phosphorylation of the matrix protease MMP14 and its lysosomal degradation. FGFR4 signaling is down-regulated by receptor internalization and degradation; MMP14 promotes internalization and degradation of FGFR4. Mutations that lead to constitutive kinase activation or impair normal FGFR4 inactivation lead to aberrant signaling.<ref>PMID:7680645</ref> <ref>PMID:7518429</ref> <ref>PMID:8663044</ref> <ref>PMID:11433297</ref> <ref>PMID:16597617</ref> <ref>PMID:17623664</ref> <ref>PMID:17311277</ref> <ref>PMID:18480409</ref> <ref>PMID:18670643</ref> <ref>PMID:20683963</ref> <ref>PMID:20018895</ref> <ref>PMID:20798051</ref> <ref>PMID:21653700</ref> <ref>PMID:20876804</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Covalent kinase inhibitors are rapidly emerging as a class of therapeutics with clinical benefits. Herein we report a series of selective 2-aminopyrimidine-based fibroblast growth factor receptor 4 (FGFR4) inhibitors exploring different types of cysteine-targeting warheads. The structure-activity relationship study revealed that the chemically tuned warheads alpha-fluoro acrylamide, vinylsulfonamide, and acetaldehyde amine were suitable as covalent warheads for the design of selective FGFR4 inhibitors. Compounds 6a, 6h, and 6i selectively suppressed FGFR4 enzymatic activity with IC50 values of 53 +/- 18, 45 +/- 11, and 16 +/- 4 nM, respectively, while sparing FGFR1/2/3. X-ray crystal structure and MALDI-TOF studies demonstrated that compound 6h bearing the alpha-fluoro acrylamide binds to FGFR4 with an irreversible binding mode, whereas compound 6i with an acetaldehyde amine binds to FGFR4 with a reversible covalent mode. 6h and 6i might provide some fundamental structural information for the rational design of new selective FGFR4 inhibitors.
		+
		+	Investigation of Covalent Warheads in the Design of 2-Aminopyrimidine-based FGFR4 Inhibitors.,Deng W, Chen X, Jiang K, Song X, Huang M, Tu ZC, Zhang Z, Lin X, Ortega R, Patterson AV, Smaill JB, Ding K, Chen S, Chen Y, Lu X ACS Med Chem Lett. 2021 Mar 22;12(4):647-652. doi:, 10.1021/acsmedchemlett.1c00052. eCollection 2021 Apr 8. PMID:33859803<ref>PMID:33859803</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dtz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen XJ]]	+	[[Category: Receptor protein-tyrosine kinase]]
-	[[Category: Chen YH]]	+	[[Category: Chen, X J]]
-	[[Category: Dai SY]]	+	[[Category: Chen, Y H]]
		+	[[Category: Dai, S Y]]
		+	[[Category: Covalent]]
		+	[[Category: Crystal]]
		+	[[Category: Inhibitor]]
		+	[[Category: Transferase]]

OCA at 06:47, 14 April 2021

2021-04-14T06:47:09Z

←Older revision		Revision as of 06:47, 14 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7dtz is ~~ON HOLD until Paper Publication~~	+	==FGFR4 complex with a covalent inhibitor==
-		+	<StructureSection load='7dtz' size='340' side='right'caption='[[7dtz]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DTZ 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=7dtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dtz OCA], [https://pdbe.org/7dtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dtz RCSB], [https://www.ebi.ac.uk/pdbsum/7dtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dtz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen XJ]]
		+	[[Category: Chen YH]]
		+	[[Category: Dai SY]]

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

2021-02-03T09:17:36Z

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

←Older revision

Revision as of 09:17, 3 February 2021

OCA: New page: '''Unreleased structure''' The entry 7dtz is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2021-02-03T09:17:35Z

New page: '''Unreleased structure''' The entry 7dtz is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7dtz is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]