166D

DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2

• PDB DOI: https://doi.org/10.2210/pdb166D/pdb
• NAKB: 166D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-03-17 Released: 1994-10-15 
• Deposition Author(s): Nunn, C.M., Jenkins, T.C., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.198 (Depositor) 
• R-Value Work: 
  0.189 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.

Nunn, C.M., Jenkins, T.C., Neidle, S.

(1994) Eur J Biochem 226: 953-961

• PubMed: 7813486 
• DOI: https://doi.org/10.1111/j.1432-1033.1994.00953.x
• Primary Citation of Related Structures:  
  166D


• PubMed Abstract: 
  

  The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.

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Organizational Affiliation: 

CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, England.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.67 kDa 
• Atom Count: 584 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PET	C [auth B]	1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE C18 H22 N4 O3 RUGJWTYDBUIXNX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.198 (Depositor) 
• R-Value Work:  0.189 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.69	α = 90
b = 40.33	β = 90
c = 66.47	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-10-15 
Deposition Author(s): Nunn, C.M., Jenkins, T.C., Neidle, S.

Revision History  

• Version 1.0: 1994-10-15
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations