328D

STRUCTURE OF A D(CGCGAATTCGCG)2-SN7167 COMPLEX

Summary for 328D

• Entry DOI: 10.2210/pdb328d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 4-[4-[2-AMINO-4-[4,6-(N-METHYLQUINOLINIUM)AMINO]BENZAMIDO]ANILINO]-N-METHYLPYRIDINIUM MESYLATE (3 entities in total)
• Functional Keywords: b-dna, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 7818.37

Authors

Squire, C.J.,Clark, G.R.,Denny, W.A. (deposition date: 1997-04-15, release date: 1997-04-23, Last modification date: 2024-04-03)

Primary citation

Squire, C.J.,Clark, G.R.,Denny, W.A.
Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.
Nucleic Acids Res., 25:4072-4078, 1997

PubMed Abstract: The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridinium ring extending as far as the C9-G16 base pair and the 1-methylquinolinium ring lying between the G4-C21 and A5-T20 base pairs. The ligand interacts only weakly with the DNA, as evidenced by long range contacts and shallow penetration into the groove. This structure is compared with that of the complex between the parent compound SN 6999 and the alkylated DNA sequence d(CGC[e6G]AATTCGCG)2. There are significant differences between the two structures in the extent of DNA bending, ligand conformation and groove binding.

PubMed: 9321660
DOI: 10.1093/nar/25.20.4072

Experimental method

X-RAY DIFFRACTION (2.6 Å)