6r1p - Revision history

OCA at 12:13, 24 January 2024

OCA — Wed, 24 Jan 2024 12:13:20 GMT

←Older revision		Revision as of 12:13, 24 January 2024
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	<StructureSection load='6r1p' size='340' side='right'caption='[[6r1p]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6r1p' size='340' side='right'caption='[[6r1p]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r1p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R1P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r1p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R1P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JPH:2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one'>JPH</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]] 1.8Å</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=6r1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1p OCA], [~~http~~://pdbe.org/6r1p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r1p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r1p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1p ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JPH:2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one'>JPH</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=6r1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1p OCA], [https://pdbe.org/6r1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r1p RCSB], [https://www.ebi.ac.uk/pdbsum/6r1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ETHR_MYCTU ETHR_MYCTU]] Involved in the repression of the monooxygenase EthA which is responsible of the formation of the active metabolite of ethionamide (ETH).<ref>PMID:10869356</ref> <ref>PMID:10944230</ref>	+	[https://www.uniprot.org/uniprot/ETHR_MYCTU ETHR_MYCTU] Involved in the repression of the monooxygenase EthA which is responsible of the formation of the active metabolite of ethionamide (ETH).<ref>PMID:10869356</ref> <ref>PMID:10944230</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6r1p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6r1p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tetracycline repressor protein 3D structures\|Tetracycline repressor protein 3D structures]]
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pohl, E~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Tatum, N~~]]	+	[[Category: Pohl E]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Tatum N]]
-	~~[[Category: Transcriptional regulator tuberculosis tetr inhibitor~~]]	+

OCA at 06:29, 19 February 2020

OCA — Wed, 19 Feb 2020 06:29:25 GMT

←Older revision		Revision as of 06:29, 19 February 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6r1p is ~~ON HOLD~~ ~~until Mar 14 2021~~	+	==EthR ligand complex==
		+	<StructureSection load='6r1p' size='340' side='right'caption='[[6r1p]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r1p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R1P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R1P FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JPH:2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one'>JPH</scene></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=6r1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r1p OCA], [http://pdbe.org/6r1p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r1p RCSB], [http://www.ebi.ac.uk/pdbsum/6r1p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r1p ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ETHR_MYCTU ETHR_MYCTU]] Involved in the repression of the monooxygenase EthA which is responsible of the formation of the active metabolite of ethionamide (ETH).<ref>PMID:10869356</ref> <ref>PMID:10944230</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.

-	~~Authors~~:	+	Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds.,Tatum NJ, Duarte F, Kamerlin SCL, Pohl E J Phys Chem Lett. 2019 May 2;10(9):2244-2249. doi: 10.1021/acs.jpclett.9b00741., Epub 2019 Apr 23. PMID:30965004<ref>PMID:30965004</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r1p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pohl, E]]
		+	[[Category: Tatum, N]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Transcriptional regulator tuberculosis tetr inhibitor]]

OCA: Protected "6r1p" [edit=sysop:move=sysop]

OCA — Wed, 20 Mar 2019 06:19:38 GMT

Protected "6r1p" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:19, 20 March 2019

OCA: New page: '''Unreleased structure''' The entry 6r1p is ON HOLD until Mar 14 2021 Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Mar 2019 06:19:36 GMT

New page: '''Unreleased structure''' The entry 6r1p is ON HOLD until Mar 14 2021 Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r1p is ON HOLD until Mar 14 2021

Authors:

Description:
[[Category: Unreleased Structures]]