1SC7

Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex

Staker, B.L.Feese, M.D.Cushman, M.Pommier, Y.Zembower, D.Stewart, L.Burgin, A.B.

(2005) J Med Chem 48: 2336-2345

  • DOI: 10.1021/jm049146p
  • Primary Citation of Related Structures:  
    1T8I, 1SC7, 1SEU

  • PubMed Abstract: 
  • Human topoisomerase I (top1) is the molecular target of a diverse set of anticancer compounds, including the camptothecins, indolocarbazoles, and indenoisoquinolines. These compounds bind to a transient top1-DNA covalent complex and inhibit the resealing of a single-strand nick that the enzyme creates to relieve superhelical tension in duplex DNA ...

    Human topoisomerase I (top1) is the molecular target of a diverse set of anticancer compounds, including the camptothecins, indolocarbazoles, and indenoisoquinolines. These compounds bind to a transient top1-DNA covalent complex and inhibit the resealing of a single-strand nick that the enzyme creates to relieve superhelical tension in duplex DNA. (Hertzberg, R. P.; et al. Biochem. 1989, 28, 4629-4638. Hsiang, Y. H.; et al. J. Biol. Chem 1985, 260, 14873-14878. Champoux, J. J. Annu. Rev. Biochem. 2001, 70, 369-413. Stewart, L.; et al. Science 1998, 729, 1534-1541.) We report the X-ray crystal structures of the human top1-DNA complex bound with camptothecin and representative members of the indenoisoquinoline and indolocarbazole classes of top1 poisons. The planar nature of all three structurally diverse classes allows them to intercalate between DNA base pairs at the site of single-strand cleavage. All three classes of compounds have a free electron pair near Arg364, a residue that if mutated confers resistance to all three classes of drugs. The common intercalative binding mode is augmented by unexpected chemotype-specific contacts with amino acid residues Asn352 and Glu356, which adopt alternative side-chain conformations to accommodate the bound compounds. These new X-ray structures explain how very different molecules can stabilize top1-DNA covalent complexes and will aid the rational design of completely novel structural classes of anticancer drugs.


    Organizational Affiliation

    deCODE BioStructures, 7869 NE Day Road West, Bainbridge Island, Washington 98110, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase ID [auth A]592Homo sapiensMutation(s): 1 
Gene Names: TOP1
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11387 (Homo sapiens)
Explore P11387 
Go to UniProtKB:  P11387
PHAROS:  P11387
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'A [auth B]10N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'B [auth C]12N/A
      Protein Feature View
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      • Reference Sequence
      Find similar nucleic acids by:  (by identity cutoff)  |  Structure
      Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3'C [auth D]22N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      M38
      Query on M38

      Download Ideal Coordinates CCD File 
      E [auth C]4-(5,11-DIOXO-5H-INDENO[1,2-C]ISOQUINOLIN-6(11H)-YL)BUTANOATE
      C20 H15 N O4
      AHIJTWCJGCWHMT-UHFFFAOYSA-N
       Ligand Interaction
      PG4
      Query on PG4

      Download Ideal Coordinates CCD File 
      F [auth A]TETRAETHYLENE GLYCOL
      C8 H18 O5
      UWHCKJMYHZGTIT-UHFFFAOYSA-N
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      PTR
      Query on PTR
      D [auth A]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      DNAIC50 :  4900   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.285 
      • R-Value Work: 0.233 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 260.94α = 90
      b = 74.659β = 96.94
      c = 57.494γ = 90
      Software Package:
      Software NamePurpose
      CNXrefinement
      HKL-2000data reduction
      SCALEPACKdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2005-04-19
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance