2ktt - Revision history

OCA at 06:48, 1 May 2024

OCA — Wed, 01 May 2024 06:48:43 GMT

←Older revision		Revision as of 06:48, 1 May 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [https://pdbe.org/2ktt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [https://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt 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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [https://pdbe.org/2ktt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [https://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A pyrrolo[2,1-c][1,4]benzodiazepine-benzimidazole hybrid (PBD-BIMZ) derived from the tricyclic anticancer PBD antibiotics can covalently bind to a guanine base at its exocyclic 2-amino group in double-helical DNA. Through the formation of stable DNA adducts, these hybrids have previously been shown to have significant anticancer activity in a number of cell lines. Here, the three-dimensional solution structure of the complex formed between the self-complementary DNA decamer 5'-AACAATTGTT-3' and PBD-BIMZ has been investigated by two-dimensional NMR spectroscopy and NOE distance restraint molecular dynamics simulations. Refinements using an explicit solvation model yielded a complex structure that is in good agreement with the NMR structural data. Successful convergence is indicated by an average mutual root-mean-square deviation of <1 A for three final representative structures selected by clustering methods from the molecular dynamics trajectories at 300 K. The ligand binds in an (11S,11aS) configuration to one of the two symmetrically located guanine bases of the duplex and is oriented with its benzimidazole moiety toward the 5'-end of the modified guanine. It is accommodated within the minor groove covering the centrally located 6 bp. Conformational and helical parameters of the DNA adduct are typical of a B-like duplex, and more significant helical distortions by the covalent binding of PBD-BIMZ are mostly confined to the covalent binding site and the junction between complexed and noncomplexed DNA segments. In contrast to the overall well-determined conformation of the bound hybrid, its terminal N-methylpiperazine ring appears to adopt various conformations associated with increased flexibility.
-
-	Solution structure of a covalently bound pyrrolo[2,1-c][1,4]benzodiazepine-benzimidazole hybrid to a 10mer DNA duplex.,Rettig M, Weingarth M, Langel W, Kamal A, Kumar PP, Weisz K Biochemistry. 2009 Dec 29;48(51):12223-32. PMID:19911838<ref>PMID:19911838</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ktt" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:25, 8 November 2023

OCA — Wed, 08 Nov 2023 17:25:48 GMT

←Older revision		Revision as of 17:25, 8 November 2023
Line 1:		Line 1:

	==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==		==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==
-	<StructureSection load='2ktt' size='340' side='right'caption='[[2ktt~~]], [[NMR_Ensembles_of_Models \| 4 NMR models~~]]' scene=''>	+	<StructureSection load='2ktt' size='340' side='right'caption='[[2ktt]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [https://pdbe.org/2ktt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [https://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt 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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [https://pdbe.org/2ktt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [https://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kamal, A]]	+	[[Category: Kamal A]]
-	[[Category: Kumar~~, P P~~]]	+	[[Category: Kumar PP]]
-	[[Category: Langel, W]]	+	[[Category: Langel W]]
-	[[Category: Rettig, M]]	+	[[Category: Rettig M]]
-	[[Category: Weingarth, M]]	+	[[Category: Weingarth M]]
-	[[Category: Weisz, K]]	+	[[Category: Weisz K]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna duplex]]~~	+
-	~~[[Category: Dna-drug complex]]~~	+
-	~~[[Category: Pbd-benzimidazole hybrid]]~~	+
-	~~[[Category: Pyrrolobenzodiazepine~~]]	+

OCA at 07:36, 2 February 2022

OCA — Wed, 02 Feb 2022 07:36:23 GMT

←Older revision		Revision as of 07:36, 2 February 2022
Line 3:		Line 3:
	<StructureSection load='2ktt' size='340' side='right'caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>		<StructureSection load='2ktt' size='340' side='right'caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2KTT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [~~http~~://pdbe.org/2ktt PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt 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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [https://pdbe.org/2ktt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [https://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:35, 29 April 2020

OCA — Wed, 29 Apr 2020 07:35:53 GMT

←Older revision		Revision as of 07:35, 29 April 2020
Line 1:		Line 1:

	==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==		==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==
-	<StructureSection load='2ktt' size='340' side='right' caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>	+	<StructureSection load='2ktt' size='340' side='right'caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KTT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://pdbe.org/2ktt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://pdbe.org/2ktt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kamal, A]]		[[Category: Kamal, A]]
	[[Category: Kumar, P P]]		[[Category: Kumar, P P]]

OCA at 08:15, 25 July 2018

OCA — Wed, 25 Jul 2018 08:15:41 GMT

←Older revision		Revision as of 08:15, 25 July 2018
Line 1:		Line 1:
		+
	==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==		==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==
	<StructureSection load='2ktt' size='340' side='right' caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>		<StructureSection load='2ktt' size='340' side='right' caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KTT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://pdbe.org/2ktt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum]</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://pdbe.org/2ktt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktt ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:19, 11 September 2015

OCA — Fri, 11 Sep 2015 09:19:49 GMT

←Older revision		Revision as of 09:19, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KTT FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum]</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://pdbe.org/2ktt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2ktt" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:49, 19 January 2015

OCA — Mon, 19 Jan 2015 16:49:59 GMT

←Older revision		Revision as of 16:49, 19 January 2015
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Kamal, A.]]	+	[[Category: Kamal, A]]
-	[[Category: Kumar, P P.]]	+	[[Category: Kumar, P P]]
-	[[Category: Langel, W.]]	+	[[Category: Langel, W]]
-	[[Category: Rettig, M.]]	+	[[Category: Rettig, M]]
-	[[Category: Weingarth, M.]]	+	[[Category: Weingarth, M]]
-	[[Category: Weisz, K.]]	+	[[Category: Weisz, K]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna duplex]]		[[Category: Dna duplex]]

OCA at 15:27, 12 October 2014

OCA — Sun, 12 Oct 2014 15:27:56 GMT

←Older revision		Revision as of 15:27, 12 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2ktt.~~png~~\|~~left\|200px~~]]	+	==Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex==
		+	<StructureSection load='2ktt' size='340' side='right' caption='[[2ktt]], [[NMR_Ensembles_of_Models \| 4 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KTT FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PBH:(11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A-HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE'>PBH</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=2ktt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ktt RCSB], [http://www.ebi.ac.uk/pdbsum/2ktt PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A pyrrolo[2,1-c][1,4]benzodiazepine-benzimidazole hybrid (PBD-BIMZ) derived from the tricyclic anticancer PBD antibiotics can covalently bind to a guanine base at its exocyclic 2-amino group in double-helical DNA. Through the formation of stable DNA adducts, these hybrids have previously been shown to have significant anticancer activity in a number of cell lines. Here, the three-dimensional solution structure of the complex formed between the self-complementary DNA decamer 5'-AACAATTGTT-3' and PBD-BIMZ has been investigated by two-dimensional NMR spectroscopy and NOE distance restraint molecular dynamics simulations. Refinements using an explicit solvation model yielded a complex structure that is in good agreement with the NMR structural data. Successful convergence is indicated by an average mutual root-mean-square deviation of <1 A for three final representative structures selected by clustering methods from the molecular dynamics trajectories at 300 K. The ligand binds in an (11S,11aS) configuration to one of the two symmetrically located guanine bases of the duplex and is oriented with its benzimidazole moiety toward the 5'-end of the modified guanine. It is accommodated within the minor groove covering the centrally located 6 bp. Conformational and helical parameters of the DNA adduct are typical of a B-like duplex, and more significant helical distortions by the covalent binding of PBD-BIMZ are mostly confined to the covalent binding site and the junction between complexed and noncomplexed DNA segments. In contrast to the overall well-determined conformation of the bound hybrid, its terminal N-methylpiperazine ring appears to adopt various conformations associated with increased flexibility.

-	~~{{STRUCTURE_2ktt\| PDB=2ktt \| SCENE= }}~~	+	Solution structure of a covalently bound pyrrolo[2,1-c][1,4]benzodiazepine-benzimidazole hybrid to a 10mer DNA duplex.,Rettig M, Weingarth M, Langel W, Kamal A, Kumar PP, Weisz K Biochemistry. 2009 Dec 29;48(51):12223-32. PMID:19911838<ref>PMID:19911838</ref>

-	~~===Solution Structure of a Covalently Bound Pyrrolo[2~~,~~1-c][1,4]benzodiazepine-Benzimidazole Hybrid to~~ a ~~10mer DNA Duplex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19911838}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2ktt]] is a 2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2KTT OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019911838<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Kamal, A.]]		[[Category: Kamal, A.]]
	[[Category: Kumar, P P.]]		[[Category: Kumar, P P.]]

OCA: Protected "2ktt" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 14:30:10 GMT

Protected "2ktt" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:30, 7 January 2013

OCA at 14:30, 7 January 2013

OCA — Mon, 07 Jan 2013 14:30:06 GMT

←Older revision		Revision as of 14:30, 7 January 2013
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-	~~{{Seed}}~~	+	[[Image:2ktt.png\|left\|200px]]
-	[[Image:2ktt.~~jpg~~\|left\|200px]]	+

-	<!--
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	{{STRUCTURE_2ktt\| PDB=2ktt \| SCENE= }}		{{STRUCTURE_2ktt\| PDB=2ktt \| SCENE= }}

	===Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex===		===Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex===

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-	<!--
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	{{ABSTRACT_PUBMED_19911838}}		{{ABSTRACT_PUBMED_19911838}}

	==About this Structure==		==About this Structure==
-	~~2KTT~~ is a 2 ~~chains~~ structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA].	+	[[2ktt]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTT OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19911838~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019911838</ref><references group="xtra"/>
	[[Category: Kamal, A.]]		[[Category: Kamal, A.]]
	[[Category: Kumar, P P.]]		[[Category: Kumar, P P.]]
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	[[Category: Pbd-benzimidazole hybrid]]		[[Category: Pbd-benzimidazole hybrid]]
	[[Category: Pyrrolobenzodiazepine]]		[[Category: Pyrrolobenzodiazepine]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 10 14:05:59 2010''