6xfp - Revision history

OCA at 14:51, 18 October 2023

2023-10-18T14:51:41Z

←Older revision		Revision as of 14:51, 18 October 2023
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	<StructureSection load='6xfp' size='340' side='right'caption='[[6xfp]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6xfp' size='340' side='right'caption='[[6xfp]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xfp]] 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=6XFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xfp]] 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=6XFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XFP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=V1Y:4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide'>V1Y</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]] 2Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRAF ([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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=V1Y:4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide'>V1Y</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=6xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xfp OCA], [https://pdbe.org/6xfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xfp RCSB], [https://www.ebi.ac.uk/pdbsum/6xfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xfp 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=6xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xfp OCA], [https://pdbe.org/6xfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xfp RCSB], [https://www.ebi.ac.uk/pdbsum/6xfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xfp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/BRAF_HUMAN BRAF_HUMAN] Note=Defects in BRAF are found in a wide range of cancers.<ref>PMID:18974108</ref> Defects in BRAF may be a cause of colorectal cancer (CRC) [MIM:[https://omim.org/entry/114500 114500].<ref>PMID:18974108</ref> Defects in BRAF are involved in lung cancer (LNCR) [MIM:[https://omim.org/entry/211980 211980]. LNCR is a common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis.<ref>PMID:18974108</ref> <ref>PMID:12460919</ref> Defects in BRAF are involved in non-Hodgkin lymphoma (NHL) [MIM:[https://omim.org/entry/605027 605027]. NHL is a cancer that starts in cells of the lymph system, which is part of the body's immune system. NHLs can occur at any age and are often marked by enlarged lymph nodes, fever and weight loss.<ref>PMID:18974108</ref> <ref>PMID:14612909</ref> Defects in BRAF are a cause of cardiofaciocutaneous syndrome (CFC syndrome) [MIM:[https://omim.org/entry/115150 115150]; also known as cardio-facio-cutaneous syndrome. CFC syndrome is characterized by a distinctive facial appearance, heart defects and mental retardation. Heart defects include pulmonic stenosis, atrial septal defects and hypertrophic cardiomyopathy. Some affected individuals present with ectodermal abnormalities such as sparse, friable hair, hyperkeratotic skin lesions and a generalized ichthyosis-like condition. Typical facial features are similar to Noonan syndrome. They include high forehead with bitemporal constriction, hypoplastic supraorbital ridges, downslanting palpebral fissures, a depressed nasal bridge, and posteriorly angulated ears with prominent helices. The inheritance of CFC syndrome is autosomal dominant.<ref>PMID:18974108</ref> Defects in BRAF are the cause of Noonan syndrome type 7 (NS7) [MIM:[https://omim.org/entry/613706 613706]. Noonan syndrome is a disorder characterized by facial dysmorphic features such as hypertelorism, a downward eyeslant and low-set posteriorly rotated ears. Other features can include short stature, a short neck with webbing or redundancy of skin, cardiac anomalies, deafness, motor delay and variable intellectual deficits.<ref>PMID:18974108</ref> <ref>PMID:19206169</ref> Defects in BRAF are the cause of LEOPARD syndrome type 3 (LEOPARD3) [MIM:[https://omim.org/entry/613707 613707]. LEOPARD3 is a disorder characterized by lentigines, electrocardiographic conduction abnormalities, ocular hypertelorism, pulmonic stenosis, abnormalities of genitalia, retardation of growth, and sensorineural deafness.<ref>PMID:18974108</ref> <ref>PMID:19206169</ref> Note=A chromosomal aberration involving BRAF is found in pilocytic astrocytomas. A tandem duplication of 2 Mb at 7q34 leads to the expression of a KIAA1549-BRAF fusion protein with a constitutive kinase activity and inducing cell transformation.<ref>PMID:18974108</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BRAF_HUMAN BRAF_HUMAN] Involved in the transduction of mitogenic signals from the cell membrane to the nucleus. May play a role in the postsynaptic responses of hippocampal neuron.
	<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 6xfp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6xfp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Serine/threonine protein kinase 3D structures\|Serine/threonine protein kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sudhamsu, J]]	+	[[Category: Sudhamsu J]]
-	[[Category: Yin, J]]	+	[[Category: Yin J]]
-	~~[[Category: Braf belvarafenib]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 12:25, 9 June 2021

2021-06-09T12:25:43Z

←Older revision		Revision as of 12:25, 9 June 2021
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	==Crystal Structure of BRAF kinase domain bound to Belvarafenib==		==Crystal Structure of BRAF kinase domain bound to Belvarafenib==
-	<StructureSection load='6xfp' size='340' side='right'caption='[[6xfp]]' scene=''>	+	<StructureSection load='6xfp' size='340' side='right'caption='[[6xfp]], [[Resolution\|resolution]] 2.00Å' 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=6XFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XFP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xfp]] 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=6XFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XFP 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=6xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xfp OCA], [https://pdbe.org/6xfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xfp RCSB], [https://www.ebi.ac.uk/pdbsum/6xfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xfp 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=V1Y:4-amino-N-{1-[(3-chloro-2-fluorophenyl)amino]-6-methylisoquinolin-5-yl}thieno[3,2-d]pyrimidine-7-carboxamide'>V1Y</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BRAF ([https://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=6xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xfp OCA], [https://pdbe.org/6xfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xfp RCSB], [https://www.ebi.ac.uk/pdbsum/6xfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xfp ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although RAF monomer inhibitors (type I.5, BRAF(V600)) are clinically approved for the treatment of BRAF(V600)-mutant melanoma, they are ineffective in non-BRAF(V600) mutant cells(1-3). Belvarafenib is a potent and selective RAF dimer (type II) inhibitor that exhibits clinical activity in patients with BRAF(V600E)- and NRAS-mutant melanomas. Here we report the first-in-human phase I study investigating the maximum tolerated dose, and assessing the safety and preliminary efficacy of belvarafenib in BRAF(V600E)- and RAS-mutated advanced solid tumours (NCT02405065, NCT03118817). By generating belvarafenib-resistant NRAS-mutant melanoma cells and analysing circulating tumour DNA from patients treated with belvarafenib, we identified new recurrent mutations in ARAF within the kinase domain. ARAF mutants conferred resistance to belvarafenib in both a dimer- and a kinase activity-dependent manner. Belvarafenib induced ARAF mutant dimers, and dimers containing mutant ARAF were active in the presence of inhibitor. ARAF mutations may serve as a general resistance mechanism for RAF dimer inhibitors as the mutants exhibit reduced sensitivity to a panel of type II RAF inhibitors. The combination of RAF plus MEK inhibition may be used to delay ARAF-driven resistance and suggests a rational combination for clinical use. Together, our findings reveal specific and compensatory functions for the ARAF isoform and implicate ARAF mutations as a driver of resistance to RAF dimer inhibitors.
		+
		+	ARAF mutations confer resistance to the RAF inhibitor belvarafenib in melanoma.,Yen I, Shanahan F, Lee J, Hong YS, Shin SJ, Moore AR, Sudhamsu J, Chang MT, Bae I, Dela Cruz D, Hunsaker T, Klijn C, Liau NPD, Lin E, Martin SE, Modrusan Z, Piskol R, Segal E, Venkatanarayan A, Ye X, Yin J, Zhang L, Kim JS, Lim HS, Kim KP, Kim YJ, Han HS, Lee SJ, Kim ST, Jung M, Hong YH, Noh YS, Choi M, Han O, Nowicka M, Srinivasan S, Yan Y, Kim TW, Malek S Nature. 2021 May 5. pii: 10.1038/s41586-021-03515-1. doi:, 10.1038/s41586-021-03515-1. PMID:33953400<ref>PMID:33953400</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xfp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Sudhamsu J]]	+	[[Category: Sudhamsu, J]]
-	[[Category: Yin J]]	+	[[Category: Yin, J]]
		+	[[Category: Braf belvarafenib]]
		+	[[Category: Signaling protein]]

OCA at 17:15, 10 March 2021

2021-03-10T17:15:00Z

←Older revision		Revision as of 17:15, 10 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xfp ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of BRAF kinase domain bound to Belvarafenib==
-		+	<StructureSection load='6xfp' size='340' side='right'caption='[[6xfp]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XFP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XFP 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=6xfp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xfp OCA], [https://pdbe.org/6xfp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xfp RCSB], [https://www.ebi.ac.uk/pdbsum/6xfp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xfp ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Sudhamsu J]]
		+	[[Category: Yin J]]

OCA at 06:39, 22 July 2020

2020-07-22T06:39:40Z

←Older revision		Revision as of 06:39, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xfp is ON HOLD	+	The entry 6xfp is ON HOLD until Paper Publication

	Authors:		Authors:

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

2020-06-24T18:28:56Z

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

←Older revision

Revision as of 18:28, 24 June 2020

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

2020-06-24T18:28:55Z

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

New page

'''Unreleased structure'''

The entry 6xfp is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]