This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
7z8w
From Proteopedia
(Difference between revisions)
(New page: ==Crystal structure of YTHDF2 with compound YLI_DC1_018== <StructureSection load='7z8w' size='340' side='right'caption='7z8w' scene=''> == Structural highlights == <table><tr><td cols...) |
|||
| (2 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
==Crystal structure of YTHDF2 with compound YLI_DC1_018== | ==Crystal structure of YTHDF2 with compound YLI_DC1_018== | ||
| - | <StructureSection load='7z8w' size='340' side='right'caption='[[7z8w]]' scene=''> | + | <StructureSection load='7z8w' size='340' side='right'caption='[[7z8w]], [[Resolution|resolution]] 1.90Å' 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=7Z8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z8W FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7z8w]] 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=7Z8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z8W 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=7z8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z8w OCA], [https://pdbe.org/7z8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z8w RCSB], [https://www.ebi.ac.uk/pdbsum/7z8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z8w ProSAT]</span></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]] 1.9Å</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=IHR:~{N}-cyclopropyl-3-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine'>IHR</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=7z8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z8w OCA], [https://pdbe.org/7z8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z8w RCSB], [https://www.ebi.ac.uk/pdbsum/7z8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z8w 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 7z8w" 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]] | ||
Current revision
Crystal structure of YTHDF2 with compound YLI_DC1_018
| |||||||||||
