459D

DNA MINOR-GROOVE RECOGNITION OF A TRIS-BENZIMIDAZOLE DRUG

Summary for 459D

• Entry DOI: 10.2210/pdb459d/pdb
• Descriptor: DNA (5'-D(*CP*GP*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3'), 2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE, ... (4 entities in total)
• Functional Keywords: minor groove binding, b-dna, complexed with tris-benzimidazole, deoxyribonucleic acid, dna
• Total number of polymer chains: 2
• Total formula weight: 7945.33

Authors

Aymami, J.,Nunn, C.M.,Neidle, S. (deposition date: 1999-03-10, release date: 1999-06-28, Last modification date: 2023-12-27)

Primary citation

Aymami, J.,Nunn, C.M.,Neidle, S.
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand.
Nucleic Acids Res., 27:2691-2698, 1999

PubMed Abstract: The crystal structure of the non-self-complementary dodecamer DNA duplex formed by d(CG[5BrC]ATAT-TTGCG) and d(CGCAAATATGCG) has been solved to 2.3 A resolution, together with that of its complex with the tris-benzimidazole minor groove binding ligand TRIBIZ. The inclusion of a bromine atom on one strand in each structure enabled the possibility of disorder to be discounted. The native structure has an exceptional narrow minor groove, of 2.5-2.6 A in the central part of the A/T region, which is increased in width by approximately 0.8 A on drug binding. The ligand molecule binds in the central part of the sequence. The benzimidazole subunits of the ligand participate in six bifurcated hydrogen bonds with A:T base pair edges, three to each DNA strand. The presence of a pair of C-H...O hydrogen bonds has been deduced from the close proximity of the pyrrolidine group of the ligand to the TpA step in the sequence.

PubMed: 10373586
DOI: 10.1093/nar/27.13.2691

Experimental method

X-RAY DIFFRACTION (2.3 Å)