1T8I

Human DNA Topoisomerase I (70 Kda) In Complex With The Poison Camptothecin and Covalent Complex With A 22 Base Pair DNA Duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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 resea ...

    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: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase IA592Homo sapiensMutation(s): 1 
Gene Names: TOP1
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
Find proteins for P11387 (Homo sapiens)
Explore P11387 
Go to UniProtKB:  P11387
NIH Common Fund Data Resources
PHAROS  P11387
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'B10N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'C12N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
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'D22N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EHD
Query on EHD

Download CCD File 
D
4-ETHYL-4-HYDROXY-1,12-DIHYDRO-4H-2-OXA-6,12A-DIAZA-DIBENZO[B,H]FLUORENE-3,13-DIONE
C20 H16 N2 O4
VSJKWCGYPAHWDS-FQEVSTJZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EHDEC50:  350   nM  BindingDB
EHDIC50:  1400   nM  BindingDB
EHDIC50:  40000   nM  BindingDB
EHDIC50:  20000   nM  BindingDB
EHDIC50:  300   nM  BindingDB
EHDIC50:  12000   nM  BindingDB
EHDIC50:  17000   nM  BindingDB
EHDIC50:  4000   nM  BindingDB
EHDIC50:  700   nM  BindingDB
EHDIC50:  679   nM  BindingDB
EHDIC50:  680   nM  BindingDB
EHDIC50:  27000   nM  BindingDB
EHDIC50:  2200   nM  BindingDB
EHDIC50:  9000   nM  BindingDB
EHDIC50:  127000   nM  BindingDB
EHDIC50:  1600   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.363α = 90
b = 114.423β = 93.49
c = 74.118γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description