367D

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

• PDB DOI: https://doi.org/10.2210/pdb367D/pdb
• NAKB: 367D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-12-19 Released: 2003-03-04 
• 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: 1.20 Å
• R-Value Observed: 0.178 

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: 4.92 kDa 
• Atom Count: 431 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DA5	C [auth A], E [auth B], F [auth B]	5-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE C18 H21 Br N4 O NROQPXQSDDINMC-UHFFFAOYSA-P
BR	D [auth A], G [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Observed: 0.178 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.096	α = 90
b = 30.096	β = 90
c = 39.547	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations