DSSR-PyMOL cartoon-block schematics: PDB entry 311d

PDB-id

311d; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.2 Å)

Summary

The role of hydrogen bonding in minor-groove drug-DNA recognition. structure of a bis-amidinium derivative of hoechst 33258 complexed to the dodecanucleotide d(cgcgaattcgcg)2

Reference

Clark GR, Boykin DW, Czarny A, Neidle S (1997): "Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition." Nucleic Acids Res., 25, 1510-1515. doi: 10.1093/nar/25.8.1510.

Abstract

The crystal structure is reported of a complex between the dodecanucleotide sequence d(CGCGAATTCGCG)2and an analogue of the DNA binding drug Hoechst 33258, in which the piperazine ring has been replaced by an amidinium group and the phenol ring by a phenylamidinium group. The structure has been refined to an R factor of 19.5% at 2.2 A resolution. The drug is held in the minor groove by five strong hydrogen bonds, together with bridging water molecules at both ends. There are few other contacts with the floor of the groove, indicating a lack of isohelicity with the groove and suggesting (i) that the observed high DNA affinity of this drug is primarily due to the array of hydrogen bonds and (ii) that these more than compensate for its poor isohelicity.