452D

ACRIDINE BINDING TO DNA

• PDB DOI: https://doi.org/10.2210/pdb452D/pdb
• NAKB: 452D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1999-02-18 Released: 2003-03-04 
• Deposition Author(s): Thorpe, J.H., Todd, A.K., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.256 
• R-Value Observed: 0.202 

Literature

Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution

Todd, A.K., Adams, A., Thorpe, J.H., Denny, W.A., Wakelin, L.P.G., Cardin, C.J.

(1999) J Med Chem 42: 536-540

• PubMed: 10052960 
• DOI: https://doi.org/10.1021/jm980479u
• Primary Citation of Related Structures:  
  366D, 367D, 452D

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Organizational Affiliation: 

Chemistry Department, University of Reading, Whiteknights, Reading RG6 6AD, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.54 kDa 
• Atom Count: 202 
• Modelled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9AD	B [auth A], C [auth A]	9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE C18 H20 N4 O YLGMVQJPGUHTRO-UHFFFAOYSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.256 
• R-Value Observed: 0.202 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.161	α = 90
b = 30.161	β = 90
c = 39.692	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-04 
Deposition Author(s): Thorpe, J.H., Todd, A.K., Cardin, C.J.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations