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[[Image:1m6f.gif|left|200px]]


{{Structure
==Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove==
|PDB= 1m6f |SIZE=350|CAPTION= <scene name='initialview01'>1m6f</scene>, resolution 1.78&Aring;
<StructureSection load='1m6f' size='340' side='right'caption='[[1m6f]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CGQ:3-[C-[N&#39;-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM'>CGQ</scene> and <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
<table><tr><td colspan='2'>[[1m6f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M6F FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CGQ:3-[C-[N-(3-CARBAMIMIDOYL-BENZYLIDENIUM)-HYDRAZINO]-[[AMINOMETHYLIDENE]AMINIUM]-IMINOMETHYL]-BENZAMIDINIUM'>CGQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1m6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m6f OCA], [https://pdbe.org/1m6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m6f RCSB], [https://www.ebi.ac.uk/pdbsum/1m6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m6f ProSAT]</span></td></tr>
 
</table>
'''Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Bailly C]]
A combination of biophysical techniques has been used to characterize the interaction of an antitrypanosomal agent, CGP 40215A, with DNA. The results from a broad array of methods (DNase I footprinting, surface plasmon resonance, X-ray crystallography, and molecular dynamics) indicate that this compound binds to the minor groove of AT DNA sequences. Despite its unusual linear shape that is not complementary to that of the DNA groove, a high binding affinity was observed in comparison with other similar but more curved diamidine compounds. The amidine groups at both ends of the ligand and the -NH groups on the linker are involved in extensive and dynamic H-bonds to the DNA bases. Complementary and consistent results were obtained from both the X-ray and molecular dynamics studies; both of these methods reveal direct and water-mediated H-bonds between the ligand and the DNA.
[[Category: Brun R]]
 
[[Category: Hamelberg D]]
==About this Structure==
[[Category: Joubert A]]
1M6F is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M6F OCA].  
[[Category: Lee MPH]]
 
[[Category: Neidle S]]
==Reference==
[[Category: Nguyen B]]
Strong binding in the DNA minor groove by an aromatic diamidine with a shape that does not match the curvature of the groove., Nguyen B, Lee MP, Hamelberg D, Joubert A, Bailly C, Brun R, Neidle S, Wilson WD, J Am Chem Soc. 2002 Nov 20;124(46):13680-1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12431090 12431090]
[[Category: Wilson WD]]
[[Category: Protein complex]]
[[Category: Bailly, C.]]
[[Category: Brun, R.]]
[[Category: Hamelberg, D.]]
[[Category: Joubert, A.]]
[[Category: Lee, M P.H.]]
[[Category: Neidle, S.]]
[[Category: Nguyen, B.]]
[[Category: Wilson, W D.]]
[[Category: CGQ]]
[[Category: MG]]
[[Category: dna-drug complex]]
[[Category: double helix]]
[[Category: minor groove binder]]
[[Category: nucleic acid]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 12:43:17 2008''

Latest revision as of 10:40, 14 February 2024

Strong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the GrooveStrong Binding in the DNA Minor Groove by an Aromatic Diamidine With a Shape That Does Not Match the Curvature of the Groove

Structural highlights

1m6f is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.78Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1m6f, resolution 1.78Å

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