6ijr: Difference between revisions

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-'''Unreleased structure'''
-The entry 6ijr is ON HOLD  until Paper Publication
+==Human PPARgamma ligand binding domain complexed with SB1495==
+<StructureSection load='6ijr' size='340' side='right'caption='[[6ijr]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6ijr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IJR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IJR FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A9C:N-{[3-({[(1S,2R)-2-{[(2E)-2-cyano-4,4-dimethylpent-2-enoyl]amino}cyclopentyl]oxy}methyl)phenyl]methyl}-4-[(4-methylpiperazin-1-yl)methyl]benzamide'>A9C</scene></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ijr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ijr OCA], [http://pdbe.org/6ijr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ijr RCSB], [http://www.ebi.ac.uk/pdbsum/6ijr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ijr ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[[http://www.uniprot.org/uniprot/PPARG_HUMAN PPARG_HUMAN]] Note=Defects in PPARG can lead to type 2 insulin-resistant diabetes and hyptertension. PPARG mutations may be associated with colon cancer.  Defects in PPARG may be associated with susceptibility to obesity (OBESITY) [MIM:[http://omim.org/entry/601665 601665]]. It is a condition characterized by an increase of body weight beyond the limitation of skeletal and physical requirements, as the result of excessive accumulation of body fat.<ref>PMID:9753710</ref>   Defects in PPARG are the cause of familial partial lipodystrophy type 3 (FPLD3) [MIM:[http://omim.org/entry/604367 604367]]. Familial partial lipodystrophies (FPLD) are a heterogeneous group of genetic disorders characterized by marked loss of subcutaneous (sc) fat from the extremities. Affected individuals show an increased preponderance of insulin resistance, diabetes mellitus and dyslipidemia.<ref>PMID:12453919</ref> <ref>PMID:11788685</ref>   Genetic variations in PPARG can be associated with susceptibility to glioma type 1 (GLM1) [MIM:[http://omim.org/entry/137800 137800]]. Gliomas are central nervous system neoplasms derived from glial cells and comprise astrocytomas, glioblastoma multiforme, oligodendrogliomas, and ependymomas. Note=Polymorphic PPARG alleles have been found to be significantly over-represented among a cohort of American patients with sporadic glioblastoma multiforme suggesting a possible contribution to disease susceptibility. [[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Note=A chromosomal aberration involving NCOA1 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with PAX3 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.
+== Function ==
+[[http://www.uniprot.org/uniprot/PPARG_HUMAN PPARG_HUMAN]] Receptor that binds peroxisome proliferators such as hypolipidemic drugs and fatty acids. Once activated by a ligand, the receptor binds to a promoter element in the gene for acyl-CoA oxidase and activates its transcription. It therefore controls the peroxisomal beta-oxidation pathway of fatty acids. Key regulator of adipocyte differentiation and glucose homeostasis. Acts as a critical regulator of gut homeostasis by suppressing NF-kappa-B-mediated proinflammatory responses.<ref>PMID:9065481</ref> <ref>PMID:16150867</ref> <ref>PMID:20829347</ref>  [[http://www.uniprot.org/uniprot/NCOA1_HUMAN NCOA1_HUMAN]] Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3.<ref>PMID:9427757</ref> <ref>PMID:7481822</ref> <ref>PMID:9223431</ref> <ref>PMID:9296499</ref> <ref>PMID:9223281</ref> <ref>PMID:10449719</ref> <ref>PMID:12954634</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peroxisome proliferator-activated receptor gamma (PPARgamma) is a major therapeutic target for the treatment of type 2 diabetes. However, the use of PPARgamma-targeted drugs, such as rosiglitazone and pioglitazone, is limited owing to serious side effects caused by classical agonism. Using a rational drug discovery approach, we recently developed SB1495, a novel reversible covalent inhibitor of the cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation of PPARgamma at Ser245, a key factor in the insulin-sensitizing effect of PPARgamma-targeted drugs. In this study, we report the crystal structures of PPARgamma in complex with SB1495 and its enantiomeric analogue SB1494, which rarely exhibits inhibitory activity, to visualize the mechanistic basis for their distinct activities. SB1495 occupies the Arm3 region near the Omega loop of the PPARgamma ligand-binding domain, whereas its enantiomeric analogue SB1494 binds to the Arm2 region. In addition, the piperazine moiety of SB1495 directly pushes the helix H2', resulting in the stabilization of the Omega loop just behind the helix H2'. Our results may contribute to the development of a new generation of antidiabetic drugs that selectively block PPARgamma phosphorylation without classical agonism.
-Authors: Jang, J.Y., Han, B.W.
+Structural basis for the inhibitory effects of a novel reversible covalent ligand on PPARgamma phosphorylation.,Jang JY, Kim H, Kim HJ, Suh SW, Park SB, Han BW Sci Rep. 2019 Aug 1;9(1):11168. doi: 10.1038/s41598-019-47672-w. PMID:31371757<ref>PMID:31371757</ref>
-Description: Human PPARgamma ligand binding domain complexed with SB1495
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Han, B.W]]
+<div class="pdbe-citations 6ijr" style="background-color:#fffaf0;"></div>
-[[Category: Jang, J.Y]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Histone acetyltransferase]]
+[[Category: Large Structures]]
+[[Category: Han, B W]]
+[[Category: Jang, J Y]]
+[[Category: Inhibitor]]
+[[Category: Ligand binding domain]]
+[[Category: Nuclear receptor]]
+[[Category: Transcription]]
+[[Category: Type 2 diabetes]]