6t07: Difference between revisions
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<StructureSection load='6t07' size='340' side='right'caption='[[6t07]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='6t07' size='340' side='right'caption='[[6t07]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6t07]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T07 FirstGlance]. <br> | <table><tr><td colspan='2'>[[6t07]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6T07 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M45:~{N}-[(2~{S})-pyrrolidin-2-yl]-1~{H}-1,2,4-triazol-5-amine'>M45</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M45:~{N}-[(2~{S})-pyrrolidin-2-yl]-1~{H}-1,2,4-triazol-5-amine'>M45</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YTHDC1, KIAA1966, YT521 ([http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6t07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t07 OCA], [http://pdbe.org/6t07 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t07 RCSB], [http://www.ebi.ac.uk/pdbsum/6t07 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t07 ProSAT]</span></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=6t07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t07 OCA], [http://pdbe.org/6t07 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t07 RCSB], [http://www.ebi.ac.uk/pdbsum/6t07 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t07 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Human]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bedi, R K]] | [[Category: Bedi, R K]] | ||
Revision as of 12:44, 1 April 2020
Crystal structure of YTHDC1 with fragment 20 (DHU_DC1_134)Crystal structure of YTHDC1 with fragment 20 (DHU_DC1_134)
Structural highlights
Function[YTDC1_HUMAN] RNA-binding protein that regulates alternative splice site selection.[1] Publication Abstract from PubMedWe 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 < 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. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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