View source for 9e5k


==env2 cobalamin riboswitch aptamer domain in complex with ethynyl-3-methylbenzene-cobalamin==
<StructureSection load='9e5k' size='340' side='right'caption='[[9e5k]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9e5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Marine_metagenome Marine metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9E5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9E5K FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1BER:[(2~{R},3~{S},4~{R},5~{S})-5-(5,6-dimethylbenzimidazol-1-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]+[(2~{R})-1-[3-[(3~{R},4~{R},5~{R},9~{S},14~{S},15~{S},19~{S},20~{S},21~{R})-4,15,20-tris(2-azanyl-2-oxidanylidene-ethyl)-9,14,19-tris(3-azanyl-3-oxidanylidene-propyl)-5,7,10,10,15,17,20,21-octamethyl-1-[2-(3-methylphenyl)ethynyl]-22-aza-2,23,24-triazonia-1$l^{5}-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaen-5-yl]propanoylamino]propan-2-yl]+hydrogen+phosphate'>A1BER</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N3D:N-METHYLPROPANE-1,3-DIAMINE'>N3D</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=9e5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9e5k OCA], [https://pdbe.org/9e5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9e5k RCSB], [https://www.ebi.ac.uk/pdbsum/9e5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9e5k ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Most RNA-binding small molecules have limited solubility, weak affinity and/or lack of specificity, restricting the medicinal chemistry often required for lead compound discovery. We reasoned that conjugation of these unfavorable ligands to a suitable 'host' molecule can solubilize the 'guest' and deliver it site-specifically to an RNA of interest to resolve these issues. Using this framework, we designed a small-molecule library that was hosted by cobalamin (Cbl) to interact with the Cbl riboswitch through a common base displacement mechanism. Combining in vitro binding, cell-based assays, chemoinformatic modeling and structure-based design, we unmasked a cryptic binding site within the riboswitch that was exploited to discover compounds that have affinity exceeding the native ligand, antagonize riboswitch function or bear no resemblance to Cbl. These data demonstrate how a privileged biphenyl-like scaffold effectively targets RNA by optimizing pi-stacking interactions within the binding pocket.

Designing small molecules targeting a cryptic RNA binding site through base displacement.,Olenginski LT, Wierzba AJ, Laursen SP, Batey RT Nat Chem Biol. 2025 Aug 29. doi: 10.1038/s41589-025-02018-8. PMID:40883492<ref>PMID:40883492</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9e5k" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Marine metagenome]]
[[Category: Batey RT]]
[[Category: Olenginski LT]]