4j7d: Difference between revisions
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==The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331== | ==The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331== | ||
<StructureSection load='4j7d' size='340' side='right' caption='[[4j7d]], [[Resolution|resolution]] 1.25Å' scene=''> | <StructureSection load='4j7d' size='340' side='right'caption='[[4j7d]], [[Resolution|resolution]] 1.25Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4j7d]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4j7d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J7D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J7D FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=I31:(4S,5R)-2-(4-TERT-BUTYL-2-ETHOXYPHENYL)-4,5-BIS(4-CHLOROPHENYL)-4,5-DIMETHYL-4,5-DIHYDRO-1H-IMIDAZOLE'>I31</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=I31:(4S,5R)-2-(4-TERT-BUTYL-2-ETHOXYPHENYL)-4,5-BIS(4-CHLOROPHENYL)-4,5-DIMETHYL-4,5-DIHYDRO-1H-IMIDAZOLE'>I31</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=4j7d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j7d OCA], [https://pdbe.org/4j7d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j7d RCSB], [https://www.ebi.ac.uk/pdbsum/4j7d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j7d ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/MDM2_XENLA MDM2_XENLA] E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degration by the proteasome (By similarity). | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 22: | Line 20: | ||
==See Also== | ==See Also== | ||
*[[MDM2|MDM2]] | *[[MDM2 3D structures|MDM2 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Xenopus laevis]] | ||
[[Category: | [[Category: Graves B]] | ||
[[Category: | [[Category: Janson C]] | ||
[[Category: | [[Category: Lukacs C]] | ||
Revision as of 13:56, 24 November 2022
The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331The 1.25A crystal structure of humanized Xenopus MDM2 with a nutlin fragment, RO5045331
Structural highlights
FunctionMDM2_XENLA E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degration by the proteasome (By similarity). Publication Abstract from PubMedProtein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments. Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor.,Fry DC, Wartchow C, Graves B, Janson C, Lukacs C, Kammlott U, Belunis C, Palme S, Klein C, Vu B ACS Med Chem Lett. 2013 May 24;4(7):660-5. doi: 10.1021/ml400062c. eCollection, 2013 Jul 11. PMID:24900726[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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