7dxl: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 7dxl is ON HOLD
+==Fragment-based Lead Discovery of Indazole-based Compounds as AXL Kinase Inhibitors==
+<StructureSection load='7dxl' size='340' side='right'caption='[[7dxl]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7dxl]] 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=7DXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DXL 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]] 3.146&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=E56:3-[4-[6-chloranyl-5-[[(3R)-pyrrolidin-3-yl]amino]-1H-indazol-3-yl]pyrazol-1-yl]benzenecarbonitrile'>E56</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=7dxl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dxl OCA], [https://pdbe.org/7dxl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dxl RCSB], [https://www.ebi.ac.uk/pdbsum/7dxl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dxl ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/MERTK_HUMAN MERTK_HUMAN] Defects in MERTK are the cause of retinitis pigmentosa type 38 (RP38) [MIM:[https://omim.org/entry/613862 613862]. RP38 is a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.<ref>PMID:11062461</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/MERTK_HUMAN MERTK_HUMAN] Receptor tyrosine kinase that transduces signals from the extracellular matrix into the cytoplasm by binding to several ligands including LGALS3, TUB, TULP1 or GAS6. Regulates many physiological processes including cell survival, migration, differentiation, and phagocytosis of apoptotic cells (efferocytosis). Ligand binding at the cell surface induces autophosphorylation of MERTK on its intracellular domain that provides docking sites for downstream signaling molecules. Following activation by ligand, interacts with GRB2 or PLCG2 and induces phosphorylation of MAPK1, MAPK2, FAK/PTK2 or RAC1. MERTK signaling plays a role in various processes such as macrophage clearance of apoptotic cells, platelet aggregation, cytoskeleton reorganization and engulfment. Functions in the retinal pigment epithelium (RPE) as a regulator of rod outer segments fragments phagocytosis. Plays also an important role in inhibition of Toll-like receptors (TLRs)-mediated innate immune response by activating STAT1, which selectively induces production of suppressors of cytokine signaling SOCS1 and SOCS3.<ref>PMID:17005688</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+AXL is a member of the TAM (TYRO3, AXL, MER) subfamily of receptor tyrosine kinases. It is upregulated in a variety of cancers and its overexpression is associated with poor disease prognosis and acquired drug resistance. Utilizing a fragment-based lead discovery approach, a new indazole-based AXL inhibitor was obtained. The indazole fragment hit 11, identified through a high concentration biochemical screen, was expeditiously improved to fragment 24 by screening our in-house expanded library of fragments (ELF) collection. Subsequent fragment optimization guided by docking studies provided potent inhibitor 54 with moderate exposure levels in mice. X-ray crystal structure of analog 50 complexed with the I650M mutated kinase domain of Mer revealed the key binding interactions for the scaffold. The good potency coupled with reasonable kinase selectivity, moderate in vivo exposure levels, and availability of structural information for the series makes it a suitable starting point for further optimization efforts.
-Authors:
+Fragment-based lead discovery of indazole-based compounds as AXL kinase inhibitors.,Ng PS, Foo K, Sim S, Wang G, Huang C, Tan LH, Poulsen A, Liu B, Tee DHY, Ahmad NHB, Wang S, Ke Z, Lee MA, Kwek ZP, Joy J, Anantharajan J, Baburajendran N, Pendharkar V, Manoharan V, Vuddagiri S, Sangthongpitag K, Hill J, Keller TH, Hung AW Bioorg Med Chem. 2021 Sep 25;49:116437. doi: 10.1016/j.bmc.2021.116437. PMID:34600239<ref>PMID:34600239</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 7dxl" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Anantharajan J]]
+[[Category: Baburajendran N]]