166D

DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2

166D の概要

• エントリーDOI: 10.2210/pdb166d/pdb
• 分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE (3 entities in total)
• 機能のキーワード: b-dna, double helix, complexed with drug, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7669.18

構造登録者

Nunn, C.M.,Jenkins, T.C.,Neidle, S. (登録日: 1994-03-17, 公開日: 1994-10-15, 最終更新日: 2024-02-07)

主引用文献

Nunn, C.M.,Jenkins, T.C.,Neidle, S.
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.
Eur.J.Biochem., 226:953-961, 1994

PubMed Abstract: The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.

PubMed: 7813486
DOI: 10.1111/j.1432-1033.1994.00953.x

実験手法

X-RAY DIFFRACTION (2.2 Å)