9z6e: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9z6e is ~~ON HOLD until Paper~~ Publication

==Crystal structure of apo LIMK1 mutant D460N==

== Structural highlights ==

<table><tr><td colspan='2'>[[9z6e]] is a 2 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=9Z6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Z6E 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]] 2.26Å</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=9z6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9z6e OCA], [https://pdbe.org/9z6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9z6e RCSB], [https://www.ebi.ac.uk/pdbsum/9z6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9z6e ProSAT]</span></td></tr>

</table>

== Disease ==

[https://www.uniprot.org/uniprot/LIMK1_HUMAN LIMK1_HUMAN] Williams syndrome. Note=LIMK1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.

== Function ==

[https://www.uniprot.org/uniprot/LIMK1_HUMAN LIMK1_HUMAN] Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics. Acts downstream of several Rho family GTPase signal transduction pathways. Activated by upstream kinases including ROCK1, PAK1 and PAK4, which phosphorylate LIMK1 on a threonine residue located in its activation loop. LIMK1 subsequently phosphorylates and inactivates the actin binding/depolymerizing factors cofilin-1/CFL1, cofilin-2/CFL2 and destrin/DSTN, thereby preventing the cleavage of filamentous actin (F-actin), and stabilizing the actin cytoskeleton. In this way LIMK1 regulates several actin-dependent biological processes including cell motility, cell cycle progression, and differentiation. Phosphorylates TPPP on serine residues, thereby promoting microtubule disassembly. Stimulates axonal outgrowth and may be involved in brain development. Isoform 3 has a dominant negative effect on actin cytoskeletal changes.<ref>PMID:10196227</ref> <ref>PMID:10436159</ref> <ref>PMID:11832213</ref> <ref>PMID:12807904</ref> <ref>PMID:15660133</ref> <ref>PMID:16230460</ref> <ref>PMID:18028908</ref>

== Publication Abstract from PubMed ==

LIM domain kinase 1 (LIMK1) has been identified as a promising therapeutic target for a variety of conditions, such as chronic pain, open-angle glaucoma, various cancers, schizophrenia, and Fragile X syndrome. However, identifying inhibitors that selectively inhibit LIMK1 over LIM domain kinase 2 (LIMK2) has proven to be challenging. A viable strategy to overcome this difficulty is the development of covalent inhibitors, which can offer both potency and selectivity for LIMK1 due to a reactive cysteine, C349, near the active site absent in its paralog LIMK2. Here we identify an irreversible covalent inhibitor of LIMK1 (cLIMK1i), which is highly selective for LIMK1 over both LIMK2 and a panel of over 100 kinases. A crystal structure of LIMK1 soaked with cLIMK1i reveals it is a type I inhibitor occupying the ATP-binding site with its acrylamide moiety oriented toward the P-loop where C349 resides. Computational modeling supports that the P-loop of LIMK1 can adopt a conformation compatible with covalent bond formation. Biochemical and biophysical characterization of the interaction of cLIMK1i with LIMK1 demonstrates that the covalent bond with LIMK1-C349 is essential for its potent inhibition. These results support covalent inhibition of LIMK1 as a viable strategy for selectively inhibiting LIMK1 over LIMK2 and other kinases.

~~Authors~~:

A covalent inhibitor targeting Cys-349 of LIMK1 confers selectivity over LIMK2.,Patteson JB, Manolaridis I, Hong MR, Johnston JM, Mesbahi-Vasey S, Gregory MC, Iwamoto DV, Reid JC, Sanders JM, Lovatt D, McDonald TP, Shurtleff VW, Gabelli SB, Bukhtiyarova M J Biol Chem. 2026 Jul 13:113322. doi: 10.1016/j.jbc.2026.113322. PMID:42442493<ref>PMID:42442493</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Bukhtiyarova M]]

[[Category: Gabelli SB]]

[[Category: Manolaridis I]]

[[Category: Patteson J]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9z6e is ON HOLD  until Paper Publication
+==Crystal structure of apo LIMK1 mutant D460N==
+<StructureSection load='9z6e' size='340' side='right'caption='[[9z6e]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9z6e]] is a 2 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=9Z6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Z6E 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]] 2.26&#8491;</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=9z6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9z6e OCA], [https://pdbe.org/9z6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9z6e RCSB], [https://www.ebi.ac.uk/pdbsum/9z6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9z6e ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/LIMK1_HUMAN LIMK1_HUMAN] Williams syndrome. Note=LIMK1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region.
+== Function ==
+[https://www.uniprot.org/uniprot/LIMK1_HUMAN LIMK1_HUMAN] Serine/threonine-protein kinase that plays an essential role in the regulation of actin filament dynamics. Acts downstream of several Rho family GTPase signal transduction pathways. Activated by upstream kinases including ROCK1, PAK1 and PAK4, which phosphorylate LIMK1 on a threonine residue located in its activation loop. LIMK1 subsequently phosphorylates and inactivates the actin binding/depolymerizing factors cofilin-1/CFL1, cofilin-2/CFL2 and destrin/DSTN, thereby preventing the cleavage of filamentous actin (F-actin), and stabilizing the actin cytoskeleton. In this way LIMK1 regulates several actin-dependent biological processes including cell motility, cell cycle progression, and differentiation. Phosphorylates TPPP on serine residues, thereby promoting microtubule disassembly. Stimulates axonal outgrowth and may be involved in brain development. Isoform 3 has a dominant negative effect on actin cytoskeletal changes.<ref>PMID:10196227</ref> <ref>PMID:10436159</ref> <ref>PMID:11832213</ref> <ref>PMID:12807904</ref> <ref>PMID:15660133</ref> <ref>PMID:16230460</ref> <ref>PMID:18028908</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+LIM domain kinase 1 (LIMK1) has been identified as a promising therapeutic target for a variety of conditions, such as chronic pain, open-angle glaucoma, various cancers, schizophrenia, and Fragile X syndrome. However, identifying inhibitors that selectively inhibit LIMK1 over LIM domain kinase 2 (LIMK2) has proven to be challenging. A viable strategy to overcome this difficulty is the development of covalent inhibitors, which can offer both potency and selectivity for LIMK1 due to a reactive cysteine, C349, near the active site absent in its paralog LIMK2. Here we identify an irreversible covalent inhibitor of LIMK1 (cLIMK1i), which is highly selective for LIMK1 over both LIMK2 and a panel of over 100 kinases. A crystal structure of LIMK1 soaked with cLIMK1i reveals it is a type I inhibitor occupying the ATP-binding site with its acrylamide moiety oriented toward the P-loop where C349 resides. Computational modeling supports that the P-loop of LIMK1 can adopt a conformation compatible with covalent bond formation. Biochemical and biophysical characterization of the interaction of cLIMK1i with LIMK1 demonstrates that the covalent bond with LIMK1-C349 is essential for its potent inhibition. These results support covalent inhibition of LIMK1 as a viable strategy for selectively inhibiting LIMK1 over LIMK2 and other kinases.
-Authors:
+A covalent inhibitor targeting Cys-349 of LIMK1 confers selectivity over LIMK2.,Patteson JB, Manolaridis I, Hong MR, Johnston JM, Mesbahi-Vasey S, Gregory MC, Iwamoto DV, Reid JC, Sanders JM, Lovatt D, McDonald TP, Shurtleff VW, Gabelli SB, Bukhtiyarova M J Biol Chem. 2026 Jul 13:113322. doi: 10.1016/j.jbc.2026.113322. PMID:42442493<ref>PMID:42442493</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9z6e" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Bukhtiyarova M]]
+[[Category: Gabelli SB]]
+[[Category: Manolaridis I]]
+[[Category: Patteson J]]