366D | pdb_0000366d

1.3 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/6-BROMO-9-AMINO-DACA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb366D/pdb
• NAKB: 366D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-12-19 Released: 1999-04-06 
• Deposition Author(s): Todd, A.K., Adams, A., Thorpe, J.H., Denny, W.A., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Work: 
  0.193 (DCC) 

Literature

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

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

(1999) J Med Chem 42: 536-540

• PubMed: 10052960 
• DOI: https://doi.org/10.1021/jm980479u
• Primary Citation 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: 2.65 kDa 
• Atom Count: 221 
• Modeled 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*(BRU)P*AP*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DA6	B [auth A], C [auth A]	6-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE C18 H21 Br N4 O HBKKAYCZISIMFL-UHFFFAOYSA-P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Work:  0.193 (DCC) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.11	α = 90
b = 30.11	β = 90
c = 39.56	γ = 120

Software Package:

Software Name	Purpose
SHELXS	phasing
SHELXL-96	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-06 
Deposition Author(s): Todd, A.K., Adams, A., Thorpe, J.H., Denny, W.A., Cardin, C.J.

Revision History  

• Version 1.0: 1999-04-06
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations