Summary information and primary citation

PDB-id
9l4e
Class
DNA
Method
NMR
Summary
Solution structure of the 2:1 complex between the benzothiazole derivative bto-28 and the myc g-quadruplex
Reference
Ni X, Hu XD, Long W, Lan W, Wang C, Wong WL, Cao C (2025): "Molecular recognition and effects of a benzothiazole derivative targeting the MYC G-quadruplex." Nucleic Acids Res., 53. doi: 10.1093/nar/gkaf888.
Abstract
 
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)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=3..- groove=---- planarity=0.181 type=other  O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2 glyco-bond=---- sugar=.... groove=---- planarity=0.123 type=planar O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3 glyco-bond=---- sugar=---. groove=---- planarity=0.139 type=planar O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,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=---- sugar=3..- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#1  pm(>>,forward)  area=13.45 rise=3.22 twist=27.3
  step#2  pm(>>,forward)  area=15.36 rise=3.50 twist=27.5
  strand#1 DNA glyco-bond=--- sugar=3.- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=--- sugar=-.. nts=3 GGG A.DG17,A.DG18,A.DG19

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2 stacking diagrams 
 1  glyco-bond=---- sugar=3..- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=13.45 rise=3.22 twist=27.3

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 2  glyco-bond=---- sugar=.... groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#2  pm(>>,forward)  area=15.36 rise=3.50 twist=27.5

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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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=---- sugar=3..- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG A.DG6,A.DG10,A.DG15,A.DG19
  step#1  pm(>>,forward)  area=13.45 rise=3.22 twist=27.3
  step#2  pm(>>,forward)  area=15.36 rise=3.50 twist=27.5
  strand#1  U DNA glyco-bond=--- sugar=3.- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2  U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  U DNA glyco-bond=--- sugar=-.. nts=3 GGG A.DG17,A.DG18,A.DG19
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=2 TA A.DT11,A.DA12
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT16

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