1PRP

CRYSTAL STRUCTURE OF D(CGCGAATTCGCG) COMPLEXED WITH PROPAMIDINE, A SHORT-CHAIN HOMOLOGUE OF THE DRUG PENTAMIDIN

Summary for 1PRP

• Entry DOI: 10.2210/pdb1prp/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 1,3-BIS(AMIDINOPHENOXY)PROPANE (3 entities in total)
• Functional Keywords: b-dna, double helix, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 7639.15

Authors

Nunn, C.M.,Jenkins, T.C.,Neidle, S. (deposition date: 1993-07-23, release date: 1994-01-15, Last modification date: 2024-02-14)

Primary citation

Nunn, C.M.,Jenkins, T.C.,Neidle, S.
Crystal structure of d(CGCGAATTCGCG) complexed with propamidine, a short-chain homologue of the drug pentamidine.
Biochemistry, 32:13838-13843, 1993

PubMed Abstract: The crystal structure of the complex between propamidine and the self-complementary DNA dodecamer d(CGCGAATTCGCG) duplex has been determined to a resolution of 2.1 A and a R-factor of 17.4%. The propamidine binds to the DNA within the minor groove, with specific hydrogen-bonding interactions from the amidinium groups to the bases and sugar groups of the DNA, via a 4-base-pair binding site. A network of water molecules lies over the mouth of the minor groove. The structure provides a rationale for the superior DNA-binding properties of propamidine as compared to pentamidine [cf. Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. This is seen to result from (i) decreased minor groove width at the binding site and (ii) reduced mobility of the bound propamidine molecule.

PubMed: 8268158
DOI: 10.1021/bi00213a012

Experimental method

X-RAY DIFFRACTION (2.1 Å)