Summary information and primary citation

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. doi: 10.1039/d0cc00221f.
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, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=ssss sugar=3333 groove=---- planarity=0.086 type=planar O- nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.063 type=planar O+ nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3 glyco-bond=---- sugar=--33 groove=---- planarity=0.122 type=planar O+ nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=ssss sugar=3333 groove=---- Major-->WC O- nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=10.57 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-- sugar=33- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- sugar=33- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4 DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG17,A.DG18,A.DG19

Download PDB file
Interactive view in 3Dmol.js
2 stacking diagrams 
 1  glyco-bond=ssss sugar=3333 groove=---- Major-->WC O- nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
  step#1  mm(<>,outward)  area=10.57 rise=4.61 twist=19.6

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ 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

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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=ssss sugar=3333 groove=---- Major-->WC O- nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG9,A.DG13,A.DG19
  step#1  mm(<>,outward)  area=10.57 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-- sugar=33- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=s-- sugar=33- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=s-- sugar=333 nts=3 GGG A.DG11,A.DG12,A.DG13
  strand#4  U DNA glyco-bond=s-- sugar=333 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