7ywb - Revision history

OCA at 13:26, 1 February 2024

2024-02-01T13:26:44Z

←Older revision		Revision as of 13:26, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ywb]] 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=7YWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YWB FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ywb]] 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=7YWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YWB 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N6M:N-METHYL-9H-PURIN-6-AMINE'>N6M</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]] 1.92Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N6M:N-METHYL-9H-PURIN-6-AMINE'>N6M</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ywb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ywb OCA], [https://pdbe.org/7ywb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ywb RCSB], [https://www.ebi.ac.uk/pdbsum/7ywb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ywb 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=7ywb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ywb OCA], [https://pdbe.org/7ywb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ywb RCSB], [https://www.ebi.ac.uk/pdbsum/7ywb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ywb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN]] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>	+	[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:30, 28 September 2022

2022-09-28T06:30:08Z

←Older revision		Revision as of 06:30, 28 September 2022
Line 1:		Line 1:

	==Crystal structure of YTHDF2 in complex with N6-Methyladenine==		==Crystal structure of YTHDF2 in complex with N6-Methyladenine==
-	<StructureSection load='7ywb' size='340' side='right'caption='[[7ywb]]' scene=''>	+	<StructureSection load='7ywb' size='340' side='right'caption='[[7ywb]], [[Resolution\|resolution]] 1.92Å' 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=7YWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YWB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ywb]] 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=7YWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YWB 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=7ywb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ywb OCA], [https://pdbe.org/7ywb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ywb RCSB], [https://www.ebi.ac.uk/pdbsum/7ywb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ywb 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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N6M:N-METHYL-9H-PURIN-6-AMINE'>N6M</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ywb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ywb OCA], [https://pdbe.org/7ywb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ywb RCSB], [https://www.ebi.ac.uk/pdbsum/7ywb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ywb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/YTHD2_HUMAN YTHD2_HUMAN]] Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability. Acts as a regulator of mRNA stability: binding to m6A-containing mRNAs results in the localization of to mRNA decay sites, such as processing bodies (P-bodies), leading to mRNA degradation.<ref>PMID:22575960</ref> <ref>PMID:24284625</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report 17 small-molecule ligands that compete with N6-methyladenosine (m(6)A) for binding to the m(6)A-reader domain of YTHDF2 (YT521-B homology domain family 2). We determined their binding mode at high resolution by X-ray crystallography and quantified their affinity by a fluorescence-based binding assay. 6-Cyclopropyluracil and a pyrazolopyrimidine derivative have favorable ligand efficiencies of 0.47 and 0.38 kcal mol(-1) per non-hydrogen atom, respectively. They represent useful starting points for hit optimization.
		+
		+	Fragment Ligands of the m(6)A-RNA Reader YTHDF2.,Nai F, Nachawati R, Zalesak F, Wang X, Li Y, Caflisch A ACS Med Chem Lett. 2022 Aug 17;13(9):1500-1509. doi:, 10.1021/acsmedchemlett.2c00303. eCollection 2022 Sep 8. PMID:36110386<ref>PMID:36110386</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ywb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Caflisch A]]		[[Category: Caflisch A]]
	[[Category: Li Y]]		[[Category: Li Y]]
	[[Category: Nai F]]		[[Category: Nai F]]

OCA at 06:19, 16 March 2022

2022-03-16T06:19:04Z

←Older revision		Revision as of 06:19, 16 March 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7ywb ~~is ON HOLD~~	+	==Crystal structure of YTHDF2 in complex with N6-Methyladenine==
-		+	<StructureSection load='7ywb' size='340' side='right'caption='[[7ywb]]' scene=''>
-	~~Authors~~: ~~Nai~~, F., Li, Y., ~~Caflisch~~, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YWB FirstGlance]. <br>
-	~~Description: Crystal structure of YTHDF2 in complex with N6-Methyladenine~~	+	</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=7ywb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ywb OCA], [https://pdbe.org/7ywb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ywb RCSB], [https://www.ebi.ac.uk/pdbsum/7ywb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ywb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Nai, F~~]]	+	__TOC__
-	[[Category: Li, Y]]	+	</StructureSection>
-	[[Category: ~~Caflisch, A~~]]	+	[[Category: Large Structures]]
		+	[[Category: Caflisch A]]
		+	[[Category: Li Y]]
		+	[[Category: Nai F]]

OCA at 05:08, 9 March 2022

2022-03-09T05:08:47Z

←Older revision		Revision as of 05:08, 9 March 2022
Line 5:		Line 5:
	Authors: Nai, F., Li, Y., Caflisch, A.		Authors: Nai, F., Li, Y., Caflisch, A.

-	Description: Crystal structure of YTHDF2 with ~~compound YLI_DC1_007~~	+	Description: Crystal structure of YTHDF2 in complex with N6-Methyladenine
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Nai, F]]		[[Category: Nai, F]]
	[[Category: Li, Y]]		[[Category: Li, Y]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]

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

2022-02-23T06:44:56Z

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

←Older revision

Revision as of 06:44, 23 February 2022

OCA: New page: '''Unreleased structure''' The entry 7ywb is ON HOLD Authors: Nai, F., Li, Y., Caflisch, A. Description: Crystal structure of YTHDF2 with compound YLI_DC1_007 [[Category: Unreleased St...

2022-02-23T06:44:55Z

New page: '''Unreleased structure''' The entry 7ywb is ON HOLD Authors: Nai, F., Li, Y., Caflisch, A. Description: Crystal structure of YTHDF2 with compound YLI_DC1_007 [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 7ywb is ON HOLD

Authors: Nai, F., Li, Y., Caflisch, A.

Description: Crystal structure of YTHDF2 with compound YLI_DC1_007
[[Category: Unreleased Structures]]
[[Category: Nai, F]]
[[Category: Li, Y]]
[[Category: Caflisch, A]]