ISDA

Deposition Date 1997-02-04

Release Date 1997-02-11

Last Version Date 2024-02-21

Entry Detail

PDB ID:

311D

Keywords:

DNA

Title:

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

Biological Source:

Source Organism:

(Taxon ID: ) (Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 21

Download Validation Report

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

HT2

Primary Citation

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.

Clark, G.R, Boykin, D.W, Czarny, A, Neidle, S.Show

Nucleic Acids Res. 25 1510 1515 (1997)

PMID: 9162901 DOI: 10.1093/nar/25.8.1510

Abstact

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sequence d(CGCGAATTCGCG)2and an analogue of the DNA binding drug Hoechst 33258, in which the piperazine ring has been replaced by an amidinium group and the phenol ring by a phenylamidinium group.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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures