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PDBsum entry 166d
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dna_rna ligands links
DNA PDB id
166d

 

 

 

 

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Contents
DNA/RNA
Ligands
PET
Waters ×73
PDB id:
166d
Name: DNA
Title: Drug-DNA minor groove recognition: crystal structure of gamma- oxapentamidine complexed with d(cgcgaattcgcg)2
Structure: DNA (5'-d( Cp Gp Cp Gp Ap Ap Tp Tp Cp Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.189     R-free:   0.198
Authors: C.M.Nunn,T.C.Jenkins,S.Neidle
Key ref: C.M.Nunn et al. (1994). Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition. Eur J Biochem, 226, 953-961. PubMed id: 7813486
Date:
17-Mar-94     Release date:   15-Oct-94    
 Headers
 References

DNA/RNA chains
  C-G-C-G-A-A-T-T-C-G-C-G 12 bases
  C-G-C-G-A-A-T-T-C-G-C-G 12 bases

 

 
Eur J Biochem 226:953-961 (1994)
PubMed id: 7813486  
 
 
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.
C.M.Nunn, T.C.Jenkins, S.Neidle.
 
  ABSTRACT  
 
The crystal structure of the complex of gamma-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG)2 has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with O4' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18798655 B.Nguyen, S.Neidle, and W.D.Wilson (2009).
A role for water molecules in DNA-ligand minor groove recognition.
  Acc Chem Res, 42, 11-21.  
10917591 Y.Zhang, A.Bell, P.S.Perlman, and M.J.Leibowitz (2000).
Pentamidine inhibits mitochondrial intron splicing and translation in Saccharomyces cerevisiae.
  RNA, 6, 937-951.  
10580832 B.S.Reddy, S.M.Sondhi, and J.W.Lown (1999).
Synthetic DNA minor groove-binding drugs.
  Pharmacol Ther, 84, 1.  
10600105 D.Vlieghe, J.Sponer, and L.Van Meervelt (1999).
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode.
  Biochemistry, 38, 16443-16451.
PDB code: 432d
9611230 A.Guerri, I.J.Simpson, and S.Neidle (1998).
Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.
  Nucleic Acids Res, 26, 2873-2878.
PDB code: 360d
  8843321 A.S.Levina, V.G.Metelev, A.S.Cohen, and P.C.Zamecnik (1996).
Conjugates of minor groove DNA binders with oligodeoxynucleotides: synthesis and properties.
  Antisense Nucleic Acid Drug Dev, 6, 75-85.  
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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