1O0K

Structure of the First Parallel DNA Quadruplex-drug Complex

• PDB DOI: https://doi.org/10.2210/pdb1O0K/pdb
• NAKB: 1O0K

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-02-22 Released: 2003-04-15 
• Deposition Author(s): Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å

Literature

Structure of the First Parallel DNA Quadruplex-drug Complex

Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

(2003) J Am Chem Soc 125: 4066-4067

• PubMed: 12670225 
• DOI: https://doi.org/10.1021/ja0297988
• Primary Citation of Related Structures:  
  1O0K


• PubMed 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.

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Organizational Affiliation: 

Department of Chemistry, University of Auckland, Auckland, New Zealand. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.17 kDa 
• Atom Count: 718 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*GP*GP*GP*T)-3'	A, B, C, D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM1	G [auth B], H [auth C], J [auth D]	DAUNOMYCIN C27 H29 N O10 STQGQHZAVUOBTE-VGBVRHCVSA-N
NA	E [auth A], F [auth A], I [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.004	α = 90
b = 47.073	β = 119.8
c = 31.865	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-15 
Deposition Author(s): Clark, G.R., Pytel, P.D., Squire, C.J., Neidle, S.

Revision History  

• Version 1.0: 2003-04-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description