DSSR-PyMOL cartoon-block schematics: PDB entry 102d

PDB-id

102d; SNAP-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.2 Å)

Summary

Sequence-dependent drug binding to the minor groove of DNA: the crystal structure of the DNA dodecamer d(cgcaaatttgcg)2 complexed with propamidine

Reference

Nunn CM, Neidle S (1995): "Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine." J.Med.Chem., 38, 2317-2325. doi: 10.1021/jm00013a008.

Abstract

The DNA-binding ligand propamidine, an analogue of the drug pentamidine which is used in the treatment of acquired immune deficiency syndrome (AIDS)-associated Pneumocystis carinii, has been cocrystallized with the DNA sequence d(CGCAAATTTGCG)2, and the crystal structure of the complex has been determined using data from 8 to 2.2 A resolution. The R factor converged to 15.5% with the inclusion of 73 water molecules. The structure shows binding of the propamidine molecule within the AT tract of the DNA minor groove with a shift from the center of the duplex toward the 3' end of ca. 2 A. The long AT tract of six base pairs in length allows the propamidine many potential binding sites in the DNA groove, and its binding is seen to occur where there is least perturbation to the DNA from that seen in the native structure. The interactions with bases are distinct from those previously observed for the sequence d(CGCGAATTCGCG)2.