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 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 

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
  • Primary Citation of Related Structures:  

  • 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 I
A
592Homo sapiensMutation(s): 0 
Gene Names: TOP1
EC: 5.99.1.2
Find proteins for P11387 (Homo sapiens)
Go to Gene View: TOP1
Go to UniProtKB:  P11387
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'B10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'C12N/A
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 SDF File 
Download CCD File 
D
4-ETHYL-4-HYDROXY-1,12-DIHYDRO-4H-2-OXA-6,12A-DIAZA-DIBENZO[B,H]FLUORENE-3,13-DIONE
CAMPTOTHECIN
C20 H16 N2 O4
VSJKWCGYPAHWDS-FQEVSTJZSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TGP
Query on TGP
C
DNA LINKINGC10 H14 N5 O6 P SDG
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EHDIC50: 12000 - 40000 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.363α = 90.00
b = 114.423β = 93.49
c = 74.118γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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