6ast - Revision history

OCA at 07:29, 1 May 2024

OCA — Wed, 01 May 2024 07:29:35 GMT

←Older revision		Revision as of 07:29, 1 May 2024
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	==NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence==		==NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence==
-	<StructureSection load='6ast' size='340' side='right'caption='[[6ast~~]], [[NMR_Ensembles_of_Models \| 11 NMR models~~]]' scene=''>	+	<StructureSection load='6ast' size='340' side='right'caption='[[6ast]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ast]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AST OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6AST FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ast]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AST OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AST FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BVV:amino(4-{[(2-{4-[amino(iminio)methyl]phenyl}-3H-imidazo[4,5-b]pyridin-5-yl)oxy]methyl}phenyl)methaniminium'>BVV</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=6ast FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ast OCA], [~~http~~://pdbe.org/6ast PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ast RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ast PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ast ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BVV:amino(4-{[(2-{4-[amino(iminio)methyl]phenyl}-3H-imidazo[4,5-b]pyridin-5-yl)oxy]methyl}phenyl)methaniminium'>BVV</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=6ast FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ast OCA], [https://pdbe.org/6ast PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ast RCSB], [https://www.ebi.ac.uk/pdbsum/6ast PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ast ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both AT and GC bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the GC base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.
-
-	First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.,Harika NK, Germann MW, Wilson WD Chemistry. 2017 Dec 11;23(69):17612-17620. doi: 10.1002/chem.201704563. Epub 2017, Nov 16. PMID:29044822<ref>PMID:29044822</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6ast" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Germann, M W~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Harika, N K~~]]	+	[[Category: Germann MW]]
-	[[Category: ~~Wilson, W D~~]]	+	[[Category: Harika NK]]
-	[[Category: ~~Dna]]~~	+	[[Category: Wilson WD]]
-	~~[[Category: Heterocyclic diamidine]]~~	+
-	~~[[Category: Minor groove binder]]~~	+
-	~~[[Category: Mixed base pair recogniition]]~~	+
-	~~[[Category: Small molecule~~]]	+

OCA at 10:05, 1 January 2020

OCA — Wed, 01 Jan 2020 10:05:29 GMT

←Older revision		Revision as of 10:05, 1 January 2020
Line 1:		Line 1:

	==NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence==		==NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence==
-	<StructureSection load='6ast' size='340' side='right' caption='[[6ast]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>	+	<StructureSection load='6ast' size='340' side='right'caption='[[6ast]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ast]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AST OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AST FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ast]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AST OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AST FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Germann, M W]]		[[Category: Germann, M W]]
	[[Category: Harika, N K]]		[[Category: Harika, N K]]

OCA at 05:57, 31 January 2018

OCA — Wed, 31 Jan 2018 05:57:04 GMT

←Older revision		Revision as of 05:57, 31 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ast is ~~ON HOLD until Paper~~ Publication	+	==NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence==
		+	<StructureSection load='6ast' size='340' side='right' caption='[[6ast]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ast]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AST OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6AST FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BVV:amino(4-{[(2-{4-[amino(iminio)methyl]phenyl}-3H-imidazo[4,5-b]pyridin-5-yl)oxy]methyl}phenyl)methaniminium'>BVV</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=6ast FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ast OCA], [http://pdbe.org/6ast PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ast RCSB], [http://www.ebi.ac.uk/pdbsum/6ast PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ast ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both AT and GC bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the GC base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.

-	~~Authors: Harika, N.K~~., Germann, M.W.~~, Wilson, W~~.D.	+	First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.,Harika NK, Germann MW, Wilson WD Chemistry. 2017 Dec 11;23(69):17612-17620. doi: 10.1002/chem.201704563. Epub 2017, Nov 16. PMID:29044822<ref>PMID:29044822</ref>

-	~~Description: NMR and Restrained Molecular Dynamics Determination~~ of the ~~Structure~~ of ~~an Aza~~-~~Benzimidazole Derivative Complex with the DNA Minor Groove of an~~ -~~AAGATA Sequence~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Wilson, W.D]]	+	<div class="pdbe-citations 6ast" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Harika, N.K~~]]	+	== References ==
-	[[Category: ~~Germann, M.W~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Germann, M W]]
		+	[[Category: Harika, N K]]
		+	[[Category: Wilson, W D]]
		+	[[Category: Dna]]
		+	[[Category: Heterocyclic diamidine]]
		+	[[Category: Minor groove binder]]
		+	[[Category: Mixed base pair recogniition]]
		+	[[Category: Small molecule]]

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

OCA — Wed, 27 Sep 2017 16:45:11 GMT

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

←Older revision

Revision as of 16:45, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6ast is ON HOLD until Paper Publication Authors: Harika, N.K., Germann, M.W., Wilson, W.D. Description: NMR and Restrained Molecular Dynamics Deter...

OCA — Wed, 27 Sep 2017 16:45:10 GMT

New page: '''Unreleased structure''' The entry 6ast is ON HOLD until Paper Publication Authors: Harika, N.K., Germann, M.W., Wilson, W.D. Description: NMR and Restrained Molecular Dynamics Deter...

New page

'''Unreleased structure'''

The entry 6ast is ON HOLD until Paper Publication

Authors: Harika, N.K., Germann, M.W., Wilson, W.D.

Description: NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence
[[Category: Unreleased Structures]]
[[Category: Wilson, W.D]]
[[Category: Harika, N.K]]
[[Category: Germann, M.W]]