ISDA: 328D

Deposition Date 1997-04-15

Release Date 1997-04-23

Last Version Date 2024-04-03

Entry Detail

PDB ID:

328D

Keywords:

DNA

Title:

STRUCTURE OF A D(CGCGAATTCGCG)2-SN7167 COMPLEX

Biological Source:

Source Organism:

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.60 Å

R-Value Free:

0.23

R-Value Work:

0.17

R-Value Observed:

0.17

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:

Ligand Molecules

SN7

Primary Citation

Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.

Squire, C.J, Clark, G.R, Denny, W.A, Gao, Y-G, Siriram, M, Denny, W.A, Wang, A.H-J.Show

Nucleic Acids Res. 25 4072 4078 (1997)

PMID: 9321660 DOI: 10.1093/nar/25.20.4072

Abstact

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.

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Primary Citation of related structures