3CDM

Structural adaptation and conservation in quadruplex-drug recognition

Summary for 3CDM

• Entry DOI: 10.2210/pdb3cdm/pdb
• Related: 3CCO
• Descriptor: DNA (5'-D(*DT*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DG)-3'), 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3-hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone, POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: quadruplex, dna, propeller, intramolecular, human telomere parallel stranded, ligand, complex
• Total number of polymer chains: 2
• Total formula weight: 18227.92

Authors

Parkinson, G.N.,Neidle, S. (deposition date: 2008-02-27, release date: 2008-09-23, Last modification date: 2023-11-01)

Primary citation

Parkinson, G.N.,Cuenca, F.,Neidle, S.
Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes
J.Mol.Biol., 381:1145-1156, 2008

PubMed Abstract: Knowledge of the biologically relevant topology is critical for the design of drugs targeting quadruplex nucleic acids. We report here crystal structures of a G-quadruplex-selective ligand complexed with two human telomeric DNA quadruplexes. The intramolecular quadruplex sequence d[TAGGG(TTAGGG)(3)] and the bimolecular quadruplex sequence d(TAGGGTTAGGGT) were co-crystallized with a tetra-substituted naphthalene diimide quadruplex-binding ligand. The structures were solved and refined to 2.10- and 2.20-A resolution, respectively, revealing that the quadruplex topology in both structures is unchanged by the addition of the ligands, retaining a parallel-stranded arrangement with external double-chain-reversal propeller loops. The parallel topology results in accessible external 5' and 3' planar G-tetrad surfaces for ligand stacking. This also enables significant ligand-induced conformational changes in several TTA propeller loops to take place such that the loops themselves are able to accommodate bound drug molecules without affecting the parallel quadruplex topology, by stacking on the external TTA connecting loop nucleotides. Ligands are bound into the external TTA loop nucleotides and stack onto G-tetrad surfaces. These crystal structures provide a framework for further ligand development of the naphthalene diimide series to enhance selectivity and affinity.

PubMed: 18619463
DOI: 10.1016/j.jmb.2008.06.022

Experimental method

X-RAY DIFFRACTION (2.1 Å)