DSSR-derived G-quadruplex features in PDB entry 2mgn
- Solution structure of a G-quadruplex bound to the bisquinolinium compound phen-dc3
- Chung, W.J., Heddi, B., Hamon, F., Teulade-Fichou, M.P., Phan, A.T.: (2014) "Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3." Angew.Chem.Int.Ed.Engl., 53, 999-1002.
- Phen-DC3 is a highly promising compound that specifically targets G-quadruplexes, with potent biological effects observed in vivo. We used NMR spectroscopy to solve the structure of the complex formed between Phen-DC3 and an intramolecular G-quadruplex derived from the c-myc promoter. Structural information revealed that Phen-DC3 interacts with the quadruplex through extensive π-stacking with guanine bases of the top G-tetrad. On the basis of our structure, modifications are proposed for the development of this compound for selective targeting of a specific G-quadruplex conformation.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU
1 glyco-bond=---- groove=---- planarity=0.314 type=other nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- groove=---- planarity=0.252 type=other nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- groove=wn-- planarity=0.493 type=other nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
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, 3 G-tetrad layers, INTRA-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.
Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
List of 1 non-stem G4-loop (including the two closing Gs)
1 type=diagonal helix=#1 nts=6 GGAAGG A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DG24