Summary information

PDB id
1o0k
Class
DNA
Method
X-ray (1.17 Å)
Summary
Structure of the first parallel DNA quadruplex-drug complex
Reference
Clark GR, Pytel PD, Squire CJ, Neidle S (2003): "Structure of the First Parallel DNA Quadruplex-drug Complex." J.Am.Chem.Soc., 125, 4066-4067. doi: 10.1021/ja0297988.
Abstract
The first crystal structure of a drug (daunomycin) bound to a parallel-stranded intermolecular telomeric G4 quadruplex (d(TGGGGT)4) has been determined to high resolution. A planar assemblage of three daunomycin molecules stacks onto the 5' end of the G4 column, with the daunosamine substituents occupying three of the four quadruplex grooves. The surface area of the terminal G-quartet in this parallel DNA quadruplex, presently occupied by three daunomycins, is sufficiently large that it could easily accommodate other potential telomerase inhibitors such as substituted porphyrins or telomestatin.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.151 type=planar nts=4 GGGG A.DG1002,D.DG1020,C.DG1014,B.DG1008
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.081 type=planar nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.193 type=bowl   nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.251 type=bowl   nts=4 GGGG A.DG1005,D.DG1023,C.DG1017,B.DG1011

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, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.DG1002,D.DG1020,C.DG1014,B.DG1008
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1005,D.DG1023,C.DG1017,B.DG1011
  step#1  pm(>>,forward)  area=7.34  rise=3.33 twist=35.8
  step#2  pm(>>,forward)  area=12.68 rise=3.30 twist=26.8
  step#3  pm(>>,forward)  area=8.95  rise=3.32 twist=30.7
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1002,A.DG1003,A.DG1004,A.DG1005
  strand#2 DNA glyco-bond=---- sugar=3--- nts=4 GGGG D.DG1020,D.DG1021,D.DG1022,D.DG1023
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG1014,C.DG1015,C.DG1016,C.DG1017
  strand#4 DNA glyco-bond=---- sugar=3--- nts=4 GGGG B.DG1008,B.DG1009,B.DG1010,B.DG1011

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3 stacking diagrams 
 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.DG1002,D.DG1020,C.DG1014,B.DG1008
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009
  step#1  pm(>>,forward)  area=7.34  rise=3.33 twist=35.8

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010
  step#2  pm(>>,forward)  area=12.68 rise=3.30 twist=26.8

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1005,D.DG1023,C.DG1017,B.DG1011
  step#3  pm(>>,forward)  area=8.95  rise=3.32 twist=30.7

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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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.DG1002,D.DG1020,C.DG1014,B.DG1008
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1003,D.DG1021,C.DG1015,B.DG1009
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1004,D.DG1022,C.DG1016,B.DG1010
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG1005,D.DG1023,C.DG1017,B.DG1011
  step#1  pm(>>,forward)  area=7.34  rise=3.33 twist=35.8
  step#2  pm(>>,forward)  area=12.68 rise=3.30 twist=26.8
  step#3  pm(>>,forward)  area=8.95  rise=3.32 twist=30.7
  strand#1  U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG1002,A.DG1003,A.DG1004,A.DG1005
  strand#2  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG D.DG1020,D.DG1021,D.DG1022,D.DG1023
  strand#3  U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG1014,C.DG1015,C.DG1016,C.DG1017
  strand#4  U DNA glyco-bond=---- sugar=3--- nts=4 GGGG B.DG1008,B.DG1009,B.DG1010,B.DG1011

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