Summary information

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, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

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List of 3 G-tetrads

 1 glyco-bond=ssss sugar=.33. groove=---- planarity=0.086 type=planar nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.063 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3 glyco-bond=---- sugar=--33 groove=---- planarity=0.122 type=planar 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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=ssss sugar=.33. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=--33 groove=---- WC-->Major 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=.3- 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=.33 nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams 
 1  glyco-bond=ssss sugar=.33. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
  step#1  mm(<>,outward)  area=10.57 rise=4.61 twist=19.6

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

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

 1  glyco-bond=ssss sugar=.33. groove=---- Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG11,A.DG17
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG12,A.DG18
 3  glyco-bond=---- sugar=--33 groove=---- WC-->Major 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=.3- 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=.33 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

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