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PDBsum entry 1d12

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dna_rna ligands metals links
DNA PDB id
1d12

 

 

 

 

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Contents
DNA/RNA
Ligands
DM2
SPM
Metals
_NA
Waters ×56
PDB id:
1d12
Name: DNA
Title: Structural comparison of anticancer drug-DNA complexes. Adriamycin and daunomycin
Structure: DNA (5'-d( Cp Gp Ap Tp Cp G)-3'). Chain: a. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.177    
Authors: C.A.Frederick,L.D.Williams,G.Ughetto,G.A.Van Der Marel,J.H.Van Boom, A.Rich,A.H.-J.Wang
Key ref:
C.A.Frederick et al. (1990). Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin. Biochemistry, 29, 2538-2549. PubMed id: 2334681 DOI: 10.1021/bi00462a016
Date:
20-Oct-89     Release date:   15-Oct-90    
 Headers
 References

DNA/RNA chain
  C-G-A-T-C-G 6 bases

 

 
DOI no: 10.1021/bi00462a016 Biochemistry 29:2538-2549 (1990)
PubMed id: 2334681  
 
 
Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin.
C.A.Frederick, L.D.Williams, G.Ughetto, G.A.van der Marel, J.H.van Boom, A.Rich, A.H.Wang.
 
  ABSTRACT  
 
The anticancer drugs adriamycin and daunomycin have each been crystallized with the DNA sequence d(CGATCG) and the three-dimensional structures of the complexes solved at 1.7- and 1.5-A resolution, respectively. These antitumor drugs have significantly different clinical properties, yet they differ chemically by only the additional hydroxyl at C14 of adriamycin. In these complexes the chromophore is intercalated at the CpG steps at either end of the DNA helix with the amino sugar extended into the minor groove. Solution of the structure of daunomycin bound to d(CGATCG) has made it possible to compare it with the previously reported structure of daunomycin bound to d(CGTACG). Although the two daunomycin complexes are similar, there is an interesting sequence dependence of the binding of the amino sugar to the A-T base pair outside the intercalation site. The complex of daunomycin with d(CGATCG) has tighter binding than the complex with d(CGTACG), leading us to infer a sequence preference in the binding of this anthracycline drug. The structures of daunomycin and adriamycin with d(CGATCG) are very similar. However, there are additional solvent interactions with the adriamycin C14 hydroxyl linking it to the DNA. Surprisingly, under the influence of the altered solvation, there is considerable difference in the conformation of spermine in these two complexes. The observed changes in the overall structures of the ternary complexes amplify the small chemical differences between these two antibiotics and provide a possible explanation for the significantly different clinical activities of these important drugs.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Cooperative effects on the formation of intercalation sites.
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PDB code: 1nab
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Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA.
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PDB code: 1jo2
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Surprising roles of electrostatic interactions in DNA-ligand complexes.
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PDB code: 1p20
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Structure of DNA-porphyrin complex.
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8662899 W.B.Cruse, P.Saludjian, Y.Leroux, G.Léger, D.E.Manouni, and T.Prangé (1996).
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  J Biol Chem, 271, 15558-15567.
PDB code: 282d
8956483 Y.Yoshikawa, K.Yoshikawa, and T.Kanbe (1996).
Daunomycin unfolds compactly packed DNA.
  Biophys Chem, 61, 93.  
7607229 C.Alhambra, F.J.Luque, J.Portugal, and M.Orozco (1995).
Molecular dynamics study of the binding of elsamicin A to DNA.
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Photoaffinity approaches to determining the sequence selectivities of DNA-small molecule interactions: actinomycin D and ethidium.
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Molecular structure of the halogenated anti-cancer drug iododoxorubicin complexed with d(TGTACA) and d(CGATCG).
  Nucleic Acids Res, 23, 4488-4494.
PDB codes: 1imr 1ims
7882991 P.F.Gallet, A.Maftah, J.M.Petit, M.Denis-Gay, and R.Julien (1995).
Direct cardiolipin assay in yeast using the red fluorescence emission of 10-N-nonyl acridine orange.
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7816639 C.Ban, B.Ramakrishnan, and M.Sundaralingam (1994).
Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing.
  Nucleic Acids Res, 22, 5466-5476.
PDB code: 100d
7738607 P.D.Grootenhuis, D.C.Roe, P.A.Kollman, and I.D.Kuntz (1994).
Finding potential DNA-binding compounds by using molecular shape.
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Polyamines, chromatin structure and transcription.
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1312486 A.Párraga, and J.Portugal (1992).
Detection of elsamicin-DNA binding specificity by restriction enzyme cleavage.
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1641324 B.Langlois d'Estaintot, B.Gallois, T.Brown, and W.N.Hunter (1992).
The molecular structure of a 4'-epiadriamycin complex with d(TGATCA) at 1.7A resolution: comparison with the structure of 4'-epiadriamycin d(TGTACA) and d(CGATCG) complexes.
  Nucleic Acids Res, 20, 3561-3566.
PDB code: 1d58
1339484 C.Bailly, J.P.Hénichart, P.Colson, and C.Houssier (1992).
Drug-DNA sequence-dependent interactions analysed by electric linear dichroism.
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Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin.
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PDB code: 1d54
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Interaction of drugs with branched DNA structures.
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1551384 M.Monnot, O.Mauffret, E.Lescot, and S.Fermandjian (1992).
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The electrostatic contribution to DNA base-stacking interactions.
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Implications and concepts of polyamine-nucleic acid interactions.
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Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex.
  Proc Natl Acad Sci U S A, 88, 2422-2426.
PDB code: 1d32
2052564 Y.G.Gao, Y.C.Liaw, Y.K.Li, G.A.van der Marel, J.H.van Boom, and A.H.Wang (1991).
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PDB codes: 1d35 1d36
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PDB code: 1d15
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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