Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
6jwe
Class
DNA
Method
NMR
Summary
Structure of ret G-quadruplex in complex with colchicine
Reference
Wang, F., Wang, C., Liu, Y., Lan, W., Han, H., Wang, R., Huang, S., Cao, C.: (2020) "Colchicine selective interaction with oncogene RET G-quadruplex revealed by NMR." Chem.Commun.(Camb.), 56, 2099-2102.
Abstract
G-quadruplexes (G4s) are frequently formed in the promoter regions of oncogenes, considered as promising drug targets for anticancer therapy. Due to high structure similarity of G4s, discovering ligands selectively interacting with only one G4 is extremely difficult. Here, mainly by NMR, we report that colchicine selectively binds to oncogene RET G4-DNA.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ssss groove=---- planarity=0.086 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2 glyco-bond=---- groove=---- planarity=0.063 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3 glyco-bond=---- groove=---- planarity=0.122 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=5.29  rise=4.61 twist=19.6
  step#2  pm(>>,forward)  area=17.30 rise=4.42 twist=21.4
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19

Download PDB file
Interactive view in 3Dmol.js

2 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
step#1 mm(<>,outward) area=5.29 rise=4.61 twist=19.6

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
step#2 pm(>>,forward) area=17.30 rise=4.42 twist=21.4

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=5.29  rise=4.61 twist=19.6
  step#2  pm(>>,forward)  area=17.30 rise=4.42 twist=21.4
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=s-- nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=s-- nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=3 GCG A.DG4,A.DC5,A.DG6
  loop#2 type=propeller strands=[#2,#3] nts=1 C A.DC10
  loop#3 type=propeller strands=[#3,#4] nts=3 GCG A.DG14,A.DC15,A.DG16

Download PDB file
Interactive view in 3Dmol.js

List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)