1L1H | pdb_00001l1h

Crystal Structure of the Quadruplex DNA-Drug Complex

• PDB DOI: https://doi.org/10.2210/pdb1L1H/pdb
• NAKB: 1L1H

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-02-16 Released: 2003-02-11 
• Deposition Author(s): Haider, S.M., Parkinson, G.N., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Structure of a G-quadruplex-Ligand Complex

Haider, S.M., Parkinson, G.N., Neidle, S.

(2003) J Mol Biology 326: 117-125

• PubMed: 12547195 
• DOI: https://doi.org/10.1016/s0022-2836(02)01354-2
• Primary Citation Related Structures: 
  1L1H


• PubMed 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.

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Organizational Affiliation: 
• Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, WC1N 1AX, London, UK.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.23 kDa 
• Atom Count: 690 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYN	C [auth A]	3-PYRROLIDIN-1-YL-N-[6-(3-PYRROLIDIN-1-YL-PROPIONYLAMINO)-ACRIDIN-3-YL]-PROPIONAMIDE C27 H33 N5 O2 WQSTTZVZUNIDBE-UHFFFAOYSA-N
K	D [auth A], E [auth A], F [auth A], G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.451	α = 90
b = 42.736	β = 90
c = 26.926	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-11 
Deposition Author(s): Haider, S.M., Parkinson, G.N., Neidle, S.

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description