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

PDB-id
1l1h
Class
DNA
Method
X-ray (1.75 Å)
Summary
Crystal structure of the quadruplex DNA-drug complex
Reference
Haider, S.M., Parkinson, G.N., Neidle, S.: (2003) "Structure of a G-quadruplex-Ligand Complex." J.Mol.Biol., 326, 117-125.
Abstract
Stabilisation of G-quadruplex structures formed from telomeric DNA, by means of quadruplex-selective ligands, is a means of inhibiting the telomerase enzyme from catalysing the synthesis of telomeric DNA repeats. In order to understand the molecular basis of ligand-quadruplex recognition, the crystal structure has been determined of such a complex, at 1.75A resolution. This complex is between a dimeric antiparallel G-quadruplex formed from the Oxytricha nova telomeric DNA sequence d(GGGGTTTTGGGG), and a di-substituted aminoalkylamido acridine compound. The structure shows that the acridine moiety is bound at one end of the stack of G-quartets, within one of the thymine loops. It is held in place by a combination of stacking interactions and specific hydrogen bonds with thymine bases. The stability of the ligand in this binding site has been confirmed by a 2ns molecular dynamics simulation.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU

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

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List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.279 type=bowl   nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2 glyco-bond=-ss- groove=w-n- planarity=0.192 type=other  nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3 glyco-bond=s--s groove=w-n- planarity=0.171 type=other  nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4 glyco-bond=-ss- groove=w-n- planarity=0.202 type=other  nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012

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

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
  step#1  mm(<>,outward)  area=14.83 rise=3.47 twist=16.2
  step#2  pp(><,inward)   area=19.13 rise=3.60 twist=37.1
  step#3  mm(<>,outward)  area=12.73 rise=3.42 twist=19.0
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
step#1 mm(<>,outward) area=14.83 rise=3.47 twist=16.2

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
step#2 pp(><,inward) area=19.13 rise=3.60 twist=37.1

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
step#3 mm(<>,outward) area=12.73 rise=3.42 twist=19.0

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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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
  step#1  mm(<>,outward)  area=14.83 rise=3.47 twist=16.2
  step#2  pp(><,inward)   area=19.13 rise=3.60 twist=37.1
  step#3  mm(<>,outward)  area=12.73 rise=3.42 twist=19.0
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT1005,A.DT1006,A.DT1007,A.DT1008
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT2005,B.DT2006,B.DT2007,B.DT2008

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

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