DSSR-derived G-quadruplex features in PDB entry 1o0k
- X-ray (1.17 Å)
- Structure of the first parallel DNA quadruplex-drug complex
- Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.: (2003) "Structure of the First Parallel DNA Quadruplex-drug Complex." J.Am.Chem.Soc., 125, 4066-4067.
- The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.151 type=planar nts=4 GGGG A.DG1002,D.DG1020,C.DG1014,B.DG1008 2 glyco-bond=---- groove=---- planarity=0.081 type=planar nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009 3 glyco-bond=---- groove=---- planarity=0.193 type=bowl nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010 4 glyco-bond=---- groove=---- planarity=0.251 type=bowl nts=4 GGGG A.DG1005,D.DG1023,C.DG1017,B.DG1011
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 4 G-tetrad layers, inter-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.