1IMS | pdb_00001ims

MOLECULAR STRUCTURE OF THE HALOGENATED ANTI-CANCER DRUG IODODOXORUBICIN COMPLEXED WITH D(TGTACA) AND D(CGATCG)

• PDB DOI: https://doi.org/10.2210/pdb1IMS/pdb
• NAKB: 1IMS

• Classification: DNA
• Mutation(s): No 


• Deposited: 1995-10-23 Released: 1996-04-04 
• Deposition Author(s): Berger, I., Su, L., Spitzner, J.R., Kang, C., Burke, T.G., Rich, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Molecular structure of the halogenated anti-cancer drug iododoxorubicin complexed with d(TGTACA) and d(CGATCG).

Berger, I., Su, L., Spitzner, J.R., Kang, C., Burke, T.G., Rich, A.

(1995) Nucleic Acids Res 23: 4488-4494

• PubMed: 7501474 
• DOI: https://doi.org/10.1093/nar/23.21.4488
• Primary Citation Related Structures: 
  1IMR, 1IMS


• PubMed Abstract: 
  

  4'-Deoxy-4'-iododoxorubicin, a halogenated anthracycline derivative, is an anticancer agent currently under Phase II clinical trials. In preclinical studies, it has demonstrated significantly reduced levels of cardiotoxicity compared to currently employed anthracyclines. It also has modified pharmacological properties resulting in an altered spectrum of experimental antitumor activity. The iodine atom at the 4' position of the sugar ring reduces the basicity and enhances the lipophilicity of this compound as compared to related anthracycline drugs. We report here single crystal X-ray diffraction studies of the complexes of 4'-deoxy-4'-iododoxorubicin with the hexanucleotide duplex sequences d(TGTACA) and d(CGATCG) at 1.6 and 1.5 A, respectively. The iodine substituent does not alter the geometry of intercalation as compared to previously solved anthracycline complexes, but appears to markedly affect the solvent environment of the structures. This could have consequences for the interaction of this drug with DNA and DNA binding proteins in cells.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.46 kDa 
• Atom Count: 211 
• 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*AP*TP*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DM7	B [auth A]	4'-DEOXY-4'-IODODOXORUBICIN C27 H29 I N O10 PDQGEKGUTOTUNV-TZSSRYMLSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.73	α = 90
b = 27.73	β = 90
c = 52.49	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-04 
Deposition Author(s): Berger, I., Su, L., Spitzner, J.R., Kang, C., Burke, T.G., Rich, A.

Revision History  

• Version 1.0: 1996-04-04
  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