1CP8

NMR STRUCTURE OF DNA (5'-D(TTGGCCAA)2-3') COMPLEXED WITH NOVEL ANTITUMOR DRUG UCH9


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Solution structure of the novel antitumor drug UCH9 complexed with d(TTGGCCAA)2 as determined by NMR.

Katahira, R.Katahira, M.Yamashita, Y.Ogawa, H.Kyogoku, Y.Yoshida, M.

(1998) Nucleic Acids Res 26: 744-755

  • DOI: 10.1093/nar/26.3.744
  • Primary Citation of Related Structures:  
    1CP8

  • PubMed Abstract: 
  • Aureolic acid group compounds, such as chromomycin A3(CHM) and mithramycin (MIT), are known as antitumor drugs. Recently we isolated a novel aureolic acid group antitumor drug, UCH9, from Streptomyces sp. The chemical structure of UCH9 is unique in that mono- (A ring) and tetrasaccharide (B-E rings) segments and a longer hydrophobic sidechain are attached to the chromophore, while di- and trisaccharide segments and a methyl group are attached to it in the cases of CHM and MIT ...

    Aureolic acid group compounds, such as chromomycin A3(CHM) and mithramycin (MIT), are known as antitumor drugs. Recently we isolated a novel aureolic acid group antitumor drug, UCH9, from Streptomyces sp. The chemical structure of UCH9 is unique in that mono- (A ring) and tetrasaccharide (B-E rings) segments and a longer hydrophobic sidechain are attached to the chromophore, while di- and trisaccharide segments and a methyl group are attached to it in the cases of CHM and MIT. It has been shown by two-dimensional agarose gel electrophoresis that the three drugs cause DNA unwinding, UCH9 causing less than the others. A photo-CIDNP experiment has revealed that UCH9 binds to the minor groove of DNA. The structure of the UCH9-d(TTGGCCAA)2 complex has been determined by 1H NMR and simulated annealing calculations. The obtained structure indicates that UCH9 binds as a dimer to the minor groove of d(TTGGCCAA)2, like CHM and MIT, but that the structural change in DNA induced on binding of UCH9 is moderate in comparison with those on binding of the other two drugs. It turns out that the dimer structure of UCH9, stabilized presumably through a hydrophobic interaction involving the A, D and E rings and the hydrophobic sidechain is different from that of CHM and thus DNA can interact with UCH9 in the minor groove with a moderate structural change.


    Organizational Affiliation

    Tokyo Research Laboratories, Kyowa Hakko Kogyo Co. Ltd, 3-6-6 Asahimachi, Machida-shi, Tokyo 194, Japan.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*TP*GP*GP*CP*CP*AP*A)-3')A, B8N/A
    Protein Feature View
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    • Reference Sequence
    Oligosaccharides

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    Entity ID: 2
    MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
    beta-D-Olivopyranose-(1-3)-2,6-dideoxy-4-O-methyl-beta-D-glucopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-OlivopyranoseC, D4N/A Oligosaccharides Interaction
    Glycosylation Resources
    GlyTouCan:  G59463XK
    GlyCosmos:  G59463XK
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DXA (Subject of Investigation/LOI)
    Query on DXA

    Download Ideal Coordinates CCD File 
    F [auth A], I [auth B]1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYDROXY-7-(SEC-BUTYL)-ANTHRACENE
    C24 H30 O7
    XGORHSPGULYMCV-HHYQQTLHSA-N
     Ligand Interaction
    DDA
    Query on DDA

    Download Ideal Coordinates CCD File 
    E [auth A], G [auth B]beta-D-Olivopyranose
    C6 H12 O4
    FDWRIIDFYSUTDP-KVTDHHQDSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    H [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Submitted: 
    • Selection Criteria: LEAST RESTRAINT VIOLATION 
    • OLDERADO: 1CP8 Olderado

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-07-01
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Atomic model, Data collection, Derived calculations, Structure summary