7z7b: Difference between revisions

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-'''Unreleased structure'''
-The entry 7z7b is ON HOLD  until Paper Publication
+==Crystal structure of YTHDF2 with compound YLI_DC1_003==
+<StructureSection load='7z7b' size='340' side='right'caption='[[7z7b]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7z7b]] 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=7Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z7B 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=OYK:~{N},9-dimethylpurin-6-amine'>OYK</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=7z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z7b OCA], [https://pdbe.org/7z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z7b RCSB], [https://www.ebi.ac.uk/pdbsum/7z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z7b ProSAT]</span></td></tr>
+</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.
-Authors: Nai, F., Li, Y., Dolbois, A., Caflisch, A.
+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>
-Description: Crystal structure of YTHDF2 with compound YLI_DC1_003
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Nai, F]]
+<div class="pdbe-citations 7z7b" style="background-color:#fffaf0;"></div>
-[[Category: Li, Y]]
+== References ==
-[[Category: Dolbois, A]]
+<references/>
-[[Category: Caflisch, A]]
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Caflisch A]]
+[[Category: Dolbois A]]
+[[Category: Li Y]]
+[[Category: Nai F]]