5GWK

Human topoisomerase IIalpha in complex with DNA and etoposide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.244 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry

Wang, Y.R.Chen, S.F.Wu, C.C.Liao, Y.W.Lin, T.S.Liu, K.T.Chen, Y.S.Li, T.K.Chien, T.C.Chan, N.L.

(2017) Nucleic Acids Res 45: 10861-10871

  • DOI: https://doi.org/10.1093/nar/gkx742
  • Primary Citation of Related Structures:  
    5GWI, 5GWJ, 5GWK

  • PubMed Abstract: 

    Human type II topoisomerase (Top2) isoforms, hTop2α and hTop2β, are targeted by some of the most successful anticancer drugs. These drugs induce Top2-mediated DNA cleavage to trigger cell-death pathways. The potency of these drugs correlates positively with their efficacy in stabilizing the enzyme-mediated DNA breaks. Structural analysis of hTop2α and hTop2β revealed the presence of methionine residues in the drug-binding pocket, we therefore tested whether a tighter Top2-drug association may be accomplished by introducing a methionine-reactive Pt2+ into a drug to further stabilize the DNA break. Herein, we synthesized an organoplatinum compound, etoplatin-N2β, by replacing the methionine-juxtaposing group of the drug etoposide with a cis-dichlorodiammineplatinum(II) moiety. Compared to etoposide, etoplatin-N2β more potently inhibits both human Top2s. While the DNA breaks arrested by etoposide can be rejoined, those captured by etoplatin-N2β are practically irreversible. Crystallographic analyses of hTop2β complexed with DNA and etoplatin-N2β demonstrate coordinate bond formation between Pt2+ and a flanking methionine. Notably, this stable coordinate tether can be loosened by disrupting the structural integrity of drug-binding pocket, suggesting that Pt2+ coordination chemistry may allow for the development of potent inhibitors with protein conformation-dependent reversibility. This approach may be exploited to achieve isoform-specific targeting of human Top2s.


  • Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 2-alpha
A, B
806Homo sapiensMutation(s): 0 
Gene Names: TOP2ATOP2
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11388 (Homo sapiens)
Explore P11388 
Go to UniProtKB:  P11388
PHAROS:  P11388
GTEx:  ENSG00000131747 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11388
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EVP
Query on EVP

Download Ideal Coordinates CCD File 
L [auth D],
N [auth F]
(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside
C29 H32 O13
VJJPUSNTGOMMGY-MRVIYFEKSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EVP BindingDB:  5GWK IC50: min: 4700, max: 1.20e+5 (nM) from 21 assay(s)
EC50: min: 810, max: 5.60e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.113α = 90
b = 126.155β = 90
c = 198.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EVPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Structure summary