7b9x: Difference between revisions
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==NMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571== | ==NMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571== | ||
<StructureSection load='7b9x' size='340' side='right'caption='[[7b9x]]' scene=''> | <StructureSection load='7b9x' size='340' side='right'caption='[[7b9x]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full | <table><tr><td colspan='2'>[[7b9x]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B9X FirstGlance]. <br> | ||
</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=7b9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b9x OCA], [https://pdbe.org/7b9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b9x RCSB], [https://www.ebi.ac.uk/pdbsum/7b9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b9x ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T52:N-{6-[3-(4-Aminobutoxy)-5-propoxyphenoxy]-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl}-3,4-dimethoxybenzene-1-sulfonamide'>T52</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/RING-type_E3_ubiquitin_transferase RING-type E3 ubiquitin transferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.27 2.3.2.27] </span></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=7b9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b9x OCA], [https://pdbe.org/7b9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b9x RCSB], [https://www.ebi.ac.uk/pdbsum/7b9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b9x ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Disease == | |||
[[https://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Defects in TRIM24 are a cause of thyroid papillary carcinoma (TPC) [MIM:[https://omim.org/entry/188550 188550]]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving TRIM24/TIF1 is found in thyroid papillary carcinomas. Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene. | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/TIF1A_HUMAN TIF1A_HUMAN]] Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity).<ref>PMID:16322096</ref> <ref>PMID:19556538</ref> <ref>PMID:21164480</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR(2)) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints, bypassing the laborious process of obtaining sequence-specific resonance assignments for the protein target. We apply this method to two therapeutic targets, the bromodomain of TRIM24 and the second bromodomain of BRD4. We show that the NMR(2) methodology can guide SBDD by rationalizing the observed SAR. We also demonstrate that new types of restraints and selective methyl labeling have the potential to dramatically reduce "time to structure" and extend the method to targets beyond the reach of traditional NMR structure elucidation. | |||
NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24.,Torres F, Walser R, Kaderli J, Rossi E, Bobby R, Packer MJ, Sarda S, Walker G, Hitchin JR, Milbradt AG, Orts J J Med Chem. 2022 Mar 31. doi: 10.1021/acs.jmedchem.1c01703. PMID:35357834<ref>PMID:35357834</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7b9x" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Milbradt | [[Category: RING-type E3 ubiquitin transferase]] | ||
[[Category: Orts J]] | [[Category: Milbradt, A G]] | ||
[[Category: Torres F]] | [[Category: Orts, J]] | ||
[[Category: Walser R]] | [[Category: Torres, F]] | ||
[[Category: Walser, R]] | |||
[[Category: Bromodomain]] | |||
[[Category: Iacs-9571]] | |||
[[Category: Nmr2]] | |||
[[Category: Oncoprotein]] | |||
[[Category: Trim24]] | |||
Revision as of 13:17, 13 April 2022
NMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571NMR2 structure of TRIM24-BD in complex with a precursor of IACS-9571
Structural highlights
Disease[TIF1A_HUMAN] Defects in TRIM24 are a cause of thyroid papillary carcinoma (TPC) [MIM:188550]. TPC is a common tumor of the thyroid that typically arises as an irregular, solid or cystic mass from otherwise normal thyroid tissue. Papillary carcinomas are malignant neoplasm characterized by the formation of numerous, irregular, finger-like projections of fibrous stroma that is covered with a surface layer of neoplastic epithelial cells. Note=A chromosomal aberration involving TRIM24/TIF1 is found in thyroid papillary carcinomas. Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene. Function[TIF1A_HUMAN] Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity).[1] [2] [3] Publication Abstract from PubMedStructure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR(2)) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints, bypassing the laborious process of obtaining sequence-specific resonance assignments for the protein target. We apply this method to two therapeutic targets, the bromodomain of TRIM24 and the second bromodomain of BRD4. We show that the NMR(2) methodology can guide SBDD by rationalizing the observed SAR. We also demonstrate that new types of restraints and selective methyl labeling have the potential to dramatically reduce "time to structure" and extend the method to targets beyond the reach of traditional NMR structure elucidation. NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24.,Torres F, Walser R, Kaderli J, Rossi E, Bobby R, Packer MJ, Sarda S, Walker G, Hitchin JR, Milbradt AG, Orts J J Med Chem. 2022 Mar 31. doi: 10.1021/acs.jmedchem.1c01703. PMID:35357834[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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