View source for 9rp7


==Crystal structure of covalent PDE6delta adduct modified by Deltafluorine (22a)==
<StructureSection load='9rp7' size='340' side='right'caption='[[9rp7]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9rp7]] is a 1 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=9RP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9RP7 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=A1JIB:~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[5-(fluoranylmethyl)-2,6-dimethyl-pyridin-3-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide'>A1JIB</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=9rp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9rp7 OCA], [https://pdbe.org/9rp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9rp7 RCSB], [https://www.ebi.ac.uk/pdbsum/9rp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9rp7 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PDE6D_HUMAN PDE6D_HUMAN] Acts as a GTP specific dissociation inhibitor (GDI). Increases the affinity of ARL3 for GTP by several orders of magnitude and does so by decreasing the nucleotide dissociation rate. Stabilizes Arl3-GTP by decreasing the nucleotide dissociation (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
For targeted covalent modification at low-reactivity carboxylates with biocompatible electrophiles, new approaches are in high demand. Engineering of the HaloTag protein facilitates such a covalent reaction between chloroalkanes and an aspartate residue. We demonstrate that conversely, engineering stable ligands can also enable covalent targeting of an acid residue in a protein binding site. Using the chaperone PDEdelta, which shuttles lipidated oncoproteins and thereby mediates their signaling activity, we show that equipping noncovalent inhibitors with a benzyl fluoride-based electrophile leads to covalent modification of a specific glutamate p.E88 in the ligand binding site. The best inhibitor, Deltafluorine, embodies a 3-fluoromethyl-pyridyl group and is stable to nucleophiles like glutathione, phosphate, acetate, and citrate. In cells, Deltafluorine combines noncovalent and covalent reactivity to demonstrate distinct cellular profiles and inhibits signaling through the MAP-kinase and Akt-mTOR pathways. In an autochthonous mouse model of highly aggressive Kras(G12D)-driven lung adenocarcinoma, Deltafluorine treatment significantly reduces tumor volume.

Targeting a Glutamic Acid in PDEdelta with Fluoromethyl-Aryl Electrophiles Impairs K-Ras Signaling.,Zhang R, Huetzen MA, Binici A, Martin-Gago P, Gasper R, Rudashevskaya E, Liu J, Nagaraju C, Reckzeh ES, Stuedle AST, Hopff AS, Mesaros A, Unger A, Thelen M, Janning P, Reinhardt HC, Ziegler S, Jachimowicz RD, Waldmann H J Med Chem. 2026 Jan 22;69(2):964-981. doi: 10.1021/acs.jmedchem.5c02082. Epub , 2026 Jan 7. PMID:41499451<ref>PMID:41499451</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9rp7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Binici A]]
[[Category: Gasper R]]
[[Category: Waldmann H]]