Detailed DSSR results for the G-quadruplex: PDB entry 5cdb
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 5cdb
- Class
- DNA
- Method
- X-ray (1.7 Å)
- Summary
- Structure of the complex of a bimolecular human telomeric DNA with a 13-diphenylalkyl berberine derivative
- Reference
- Ferraroni M, Bazzicalupi C, Papi F, Fiorillo G, Guaman-Ortiz LM, Nocentini A, Scovassi AI, Lombardi P, Gratteri P (2016): "Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes." Chem Asian J, 11, 1107-1115. doi: 10.1002/asia.201600116.
- Abstract
- The interaction between 13-phenylalkyl and 13-diphenylalkyl berberine derivatives (NAX) and human telomeric DNA G4 structures has been investigated by both spectroscopic and crystallographic methods. NAX042 and NAX053 are the best compounds improving the performance of the natural precursor berberine. This finding is in agreement with the X-ray diffraction result for the NAX053-Tel12 adduct, showing the ligand which interacts via π-stacking, sandwiched at the interface of two symmetry-related quadruplex units, with its benzhydryl group contributing to the overall stability of the adduct by means of additional π-stacking interactions with the DNA residues. The berberine derivatives were also investigated for their cytotoxic activity towards a panel of human cancer cell lines. Compounds NAX042 and NAX053 affect the viability of cancer cell lines in a dose-dependent manner.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.175 type=bowl-2 nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- planarity=0.148 type=planar nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- planarity=0.301 type=bowl nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23
List of 1 G4-helix
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, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=10.18 rise=3.32 twist=29.8 step#2 pm(>>,forward) area=12.49 rise=3.45 twist=26.6 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG21,B.DG22,B.DG23 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 |
List of 1 G4-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, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,B.DG15,B.DG21 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,B.DG16,B.DG22 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,B.DG17,B.DG23 step#1 pm(>>,forward) area=10.18 rise=3.32 twist=29.8 step#2 pm(>>,forward) area=12.49 rise=3.45 twist=26.6 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG21,B.DG22,B.DG23 loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA B.DT18,B.DT19,B.DA20 |