6t02: Difference between revisions

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-'''Unreleased structure'''
-The entry 6t02 is ON HOLD  until Oct 02 2021
+==Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169)==
+<StructureSection load='6t02' size='340' side='right'caption='[[6t02]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6t02]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T02 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T02 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M5E:(~{S})-phenyl-[(2~{S})-pyrrolidin-2-yl]methanol'>M5E</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6t02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t02 OCA], [http://pdbe.org/6t02 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t02 RCSB], [http://www.ebi.ac.uk/pdbsum/6t02 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t02 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/YTDC1_HUMAN YTDC1_HUMAN]] RNA-binding protein that regulates alternative splice site selection.<ref>PMID:20167602</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report a crystallographic analysis of small-molecule ligands of the human YTHDC1 domain that recognizes N6-methylated adenine (m(6)A) in RNA. The 30 binders are fragments (molecular weight &lt; 300 g mol(-1)) that represent 10 different chemotypes identified by virtual screening. Despite the structural disorder of the binding site loop (residues 429-439), most of the 30 fragments emulate the two main interactions of the -NHCH3 group of m(6)A. These interactions are the hydrogen bond to the backbone carbonyl of Ser378 and the van der Waals contacts with the tryptophan cage. Different chemical groups are involved in the conserved binding motifs. Some of the fragments show favorable ligand efficiency for YTHDC1 and selectivity against other m(6)A reader domains. The structural information is useful for the design of modulators of m(6)A recognition by YTHDC1.
-Authors: Bedi, R.K., Huang, D., Sledz, P., Caflisch, A.
+Selectively Disrupting m(6)A-Dependent Protein-RNA Interactions with Fragments.,Bedi RK, Huang D, Wiedmer L, Li Y, Dolbois A, Wojdyla JA, Sharpe ME, Caflisch A, Sledz P ACS Chem Biol. 2020 Mar 2. doi: 10.1021/acschembio.9b00894. PMID:32101404<ref>PMID:32101404</ref>
-Description: Crystal structure of YTHDC1 with fragment 15 (DHU_DC1_169)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 6t02" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Bedi, R K]]
 [[Category: Caflisch, A]]
+[[Category: Huang, D]]
 [[Category: Sledz, P]]
-[[Category: Bedi, R.K]]
+[[Category: Complex]]
-[[Category: Huang, D]]
+[[Category: Epitranscriptomic]]
+[[Category: Fragment]]
+[[Category: Rna binding protein]]
+[[Category: Ythdc1]]