8a32 - Revision history

OCA at 13:36, 1 February 2024

2024-02-01T13:36:23Z

← Older revision		Revision as of 13:36, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8a32]] 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=8A32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A32 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8a32]] 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=8A32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A32 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KVA:4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic+acid'>KVA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.47Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KVA:4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic+acid'>KVA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8a32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a32 OCA], [https://pdbe.org/8a32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a32 RCSB], [https://www.ebi.ac.uk/pdbsum/8a32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a32 ProSAT]</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=8a32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a32 OCA], [https://pdbe.org/8a32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a32 RCSB], [https://www.ebi.ac.uk/pdbsum/8a32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a32 ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 8a32" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 8a32" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[P53 3D structures\|P53 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:44, 30 November 2022

2022-11-30T10:44:35Z

← Older revision		Revision as of 10:44, 30 November 2022
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	~~'''Unreleased structure'''~~

	The entry ~~8a32~~ is ~~ON HOLD~~ ~~until Paper~~ Publication		==p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769==
			<StructureSection load='8a32' size='340' side='right'caption='[[8a32]], [[Resolution\|resolution]] 1.47Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8a32]] 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=8A32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A32 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KVA:4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic+acid'>KVA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=8a32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a32 OCA], [https://pdbe.org/8a32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a32 RCSB], [https://www.ebi.ac.uk/pdbsum/8a32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a32 ProSAT]</span></td></tr>
			</table>
			== Disease ==
			[https://www.uniprot.org/uniprot/P53_HUMAN P53_HUMAN] Note=TP53 is found in increased amounts in a wide variety of transformed cells. TP53 is frequently mutated or inactivated in about 60% of cancers. TP53 defects are found in Barrett metaplasia a condition in which the normally stratified squamous epithelium of the lower esophagus is replaced by a metaplastic columnar epithelium. The condition develops as a complication in approximately 10% of patients with chronic gastroesophageal reflux disease and predisposes to the development of esophageal adenocarcinoma. Defects in TP53 are a cause of esophageal cancer (ESCR) [MIM:[https://omim.org/entry/133239 133239]. Defects in TP53 are a cause of Li-Fraumeni syndrome (LFS) [MIM:[https://omim.org/entry/151623 151623]. LFS is an autosomal dominant familial cancer syndrome that in its classic form is defined by the existence of a proband affected by a sarcoma before 45 years with a first degree relative affected by any tumor before 45 years and another first degree relative with any tumor before 45 years or a sarcoma at any age. Other clinical definitions for LFS have been proposed (PubMed:8118819 and PubMed:8718514) and called Li-Fraumeni like syndrome (LFL). In these families affected relatives develop a diverse set of malignancies at unusually early ages. Four types of cancers account for 80% of tumors occurring in TP53 germline mutation carriers: breast cancers, soft tissue and bone sarcomas, brain tumors (astrocytomas) and adrenocortical carcinomas. Less frequent tumors include choroid plexus carcinoma or papilloma before the age of 15, rhabdomyosarcoma before the age of 5, leukemia, Wilms tumor, malignant phyllodes tumor, colorectal and gastric cancers.<ref>PMID:10570149</ref> <ref>PMID:1933902</ref> <ref>PMID:1978757</ref> <ref>PMID:2259385</ref> <ref>PMID:1737852</ref> <ref>PMID:1565144</ref> <ref>PMID:7887414</ref> <ref>PMID:8825920</ref> <ref>PMID:9452042</ref> <ref>PMID:10484981</ref> Defects in TP53 are involved in head and neck squamous cell carcinomas (HNSCC) [MIM:[https://omim.org/entry/275355 275355]; also known as squamous cell carcinoma of the head and neck. Defects in TP53 are a cause of lung cancer (LNCR) [MIM:[https://omim.org/entry/211980 211980]. LNCR is a common malignancy affecting tissues of the lung. The most common form of lung cancer is non-small cell lung cancer (NSCLC) that can be divided into 3 major histologic subtypes: squamous cell carcinoma, adenocarcinoma, and large cell lung cancer. NSCLC is often diagnosed at an advanced stage and has a poor prognosis. Defects in TP53 are a cause of choroid plexus papilloma (CPLPA) [MIM:[https://omim.org/entry/260500 260500]. Choroid plexus papilloma is a slow-growing benign tumor of the choroid plexus that often invades the leptomeninges. In children it is usually in a lateral ventricle but in adults it is more often in the fourth ventricle. Hydrocephalus is common, either from obstruction or from tumor secretion of cerebrospinal fluid. If it undergoes malignant transformation it is called a choroid plexus carcinoma. Primary choroid plexus tumors are rare and usually occur in early childhood.<ref>PMID:12085209</ref> Defects in TP53 are a cause of adrenocortical carcinoma (ADCC) [MIM:[https://omim.org/entry/202300 202300]. ADCC is a rare childhood tumor of the adrenal cortex. It occurs with increased frequency in patients with the Beckwith-Wiedemann syndrome and is a component tumor in Li-Fraumeni syndrome.<ref>PMID:11481490</ref> Defects in TP53 are the cause of susceptibility to basal cell carcinoma 7 (BCC7) [MIM:[https://omim.org/entry/614740 614740]. A common malignant skin neoplasm that typically appears on hair-bearing skin, most commonly on sun-exposed areas. It is slow growing and rarely metastasizes, but has potentialities for local invasion and destruction. It usually develops as a flat, firm, pale area that is small, raised, pink or red, translucent, shiny, and waxy, and the area may bleed following minor injury. Tumor size can vary from a few millimeters to several centimeters in diameter.<ref>PMID:21946351</ref>
			== Function ==
			[https://www.uniprot.org/uniprot/P53_HUMAN P53_HUMAN] Acts as a tumor suppressor in many tumor types; induces growth arrest or apoptosis depending on the physiological circumstances and cell type. Involved in cell cycle regulation as a trans-activator that acts to negatively regulate cell division by controlling a set of genes required for this process. One of the activated genes is an inhibitor of cyclin-dependent kinases. Apoptosis induction seems to be mediated either by stimulation of BAX and FAS antigen expression, or by repression of Bcl-2 expression. In cooperation with mitochondrial PPIF is involved in activating oxidative stress-induced necrosis; te function is largely independent of transcription. Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA-Mkln1. LincRNA-p21 participates in TP53-dependent transcriptional repression leading to apoptosis and seem to have to effect on cell-cycle regulation. Implicated in Notch signaling cross-over. Prevents CDK7 kinase activity when associated to CAK complex in response to DNA damage, thus stopping cell cycle progression. Isoform 2 enhances the transactivation activity of isoform 1 from some but not all TP53-inducible promoters. Isoform 4 suppresses transactivation activity and impairs growth suppression mediated by isoform 1. Isoform 7 inhibits isoform 1-mediated apoptosis.<ref>PMID:9840937</ref> <ref>PMID:11025664</ref> <ref>PMID:12810724</ref> <ref>PMID:15186775</ref> <ref>PMID:15340061</ref> <ref>PMID:17317671</ref> <ref>PMID:17349958</ref> <ref>PMID:19556538</ref> <ref>PMID:20673990</ref> <ref>PMID:20959462</ref> <ref>PMID:22726440</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The tumor suppressor protein p53 is inactivated in the majority of human cancers and remains a prime target for developing new drugs to reactivate its tumor suppressing activity for anticancer therapies. The oncogenic p53 mutant Y220C accounts for approximately 125,000 new cancer cases per annum and is one of the most prevalent p53 mutants overall. It harbors a narrow, mutationally induced pocket at the surface of the DNA-binding domain that destabilizes p53, leading to its rapid denaturation and aggregation. Here, we present the structure-guided development of high-affinity small molecules stabilizing p53-Y220C in vitro, along with the synthetic routes developed in the process, in vitro structure-activity relationship data, and confirmation of their binding mode by protein X-ray crystallography. We disclose two new chemical probes displaying sub-micromolar binding affinity in vitro, marking an important milestone since the discovery of the first small-molecule ligand of Y220C in 2008. New chemical probe JC744 displayed a K (d) = 320 nM, along with potent in vitro protein stabilization. This study, therefore, represents a significant advance toward high-affinity Y220C ligands for clinical evaluation.

	~~Authors: Balourdas, D.I~~., Stephenson Clarke, J.R., Baud~~, M~~.G.J.~~, Knapp, S~~.~~, Joerger, A~~.C.~~, Structural Genomics Consortium (SGC)~~		Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic p53 Mutant Y220C.,Stephenson Clarke JR, Douglas LR, Duriez PJ, Balourdas DI, Joerger AC, Khadiullina R, Bulatov E, Baud MGJ ACS Pharmacol Transl Sci. 2022 Oct 11;5(11):1169-1180. doi: , 10.1021/acsptsci.2c00164. eCollection 2022 Nov 11. PMID:36407959<ref>PMID:36407959</ref>

	~~Description: p53 cancer mutant Y220C in complex with iodophenol~~-~~based small~~-~~molecule stabilizer JC769~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased Structures~~]]		</div>
	[[Category: ~~Knapp, S~~]]		<div class="pdbe-citations 8a32" style="background-color:#fffaf0;"></div>
	[[Category: Balourdas~~, D.I~~]]		== References ==
	[[Category: ~~Joerger, A.C~~]]		<references/>
	[[Category: ~~Structural Genomics Consortium (Sgc)~~]]		__TOC__
	[[Category: ~~Baud, M.G.J~~]]		</StructureSection>
	[[Category: Stephenson Clarke~~, J.R~~]]		[[Category: Homo sapiens]]
			[[Category: Large Structures]]
			[[Category: Balourdas DI]]
			[[Category: Baud MGJ]]
			[[Category: Joerger AC]]
			[[Category: Knapp S]]
			[[Category: Stephenson Clarke JR]]

OCA at 04:06, 13 July 2022

2022-07-13T04:06:01Z

← Older revision		Revision as of 04:06, 13 July 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8a32 is ON HOLD		The entry 8a32 is ON HOLD until Paper Publication

	Authors: Balourdas, D.I., Stephenson Clarke, J.R., Baud, M.G.J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)		Authors: Balourdas, D.I., Stephenson Clarke, J.R., Baud, M.G.J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)

OCA: Protected "8a32" [edit=sysop:move=sysop]

2022-06-15T04:06:35Z

Protected "8a32" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:06, 15 June 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8a32 is ON HOLD Authors: Balourdas, D.I., Stephenson Clarke, J.R., Baud, M.G.J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC) Des...

2022-06-15T04:06:34Z

New page: '''Unreleased structure''' The entry 8a32 is ON HOLD Authors: Balourdas, D.I., Stephenson Clarke, J.R., Baud, M.G.J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC) Des...

New page

'''Unreleased structure'''

The entry 8a32 is ON HOLD

Authors: Balourdas, D.I., Stephenson Clarke, J.R., Baud, M.G.J., Knapp, S., Joerger, A.C., Structural Genomics Consortium (SGC)

Description: p53 cancer mutant Y220C in complex with iodophenol-based small-molecule stabilizer JC769
[[Category: Unreleased Structures]]
[[Category: Knapp, S]]
[[Category: Balourdas, D.I]]
[[Category: Joerger, A.C]]
[[Category: Structural Genomics Consortium (Sgc)]]
[[Category: Baud, M.G.J]]
[[Category: Stephenson Clarke, J.R]]