1K4T

HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.269 (Depositor) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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

This is version 1.4 of the entry. See complete history


Literature

The mechanism of topoisomerase I poisoning by a camptothecin analog

Staker, B.L.Hjerrild, K.Feese, M.D.Behnke, C.A.Burgin Jr., A.B.Stewart, L.J.

(2002) Proc Natl Acad Sci U S A 99: 15387-15392

  • DOI: https://doi.org/10.1073/pnas.242259599
  • Primary Citation of Related Structures:  
    1K4S, 1K4T

  • PubMed Abstract: 

    We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (-1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme-substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure-activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site.


  • Organizational Affiliation

    deCODE genetics, Incorporated, BioStructures Group, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase ID [auth A]592Homo sapiensMutation(s): 1 
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
GTEx:  ENSG00000198900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11387
Sequence Annotations
Expand
  • Reference Sequence
1K4T_4
050100150200250300350400450500550
1K4T_4
UNIPROT P11387
UNMODELED
MUTATION
MODIFIED MONOMER
HYDROPATHY
DISORDER
DISORDERED BINDING
PFAM
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTG
Query on TTG

Download Ideal Coordinates CCD File 
E [auth C]2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID
C23 H25 N3 O6
DPQJTQJZJNYUEC-QHCPKHFHSA-N
TTC
Query on TTC

Download Ideal Coordinates CCD File 
F [auth D](S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE
C23 H23 N3 O5
UCFGDBYHRUNTLO-QHCPKHFHSA-N
HG
Query on HG

Download Ideal Coordinates CCD File 
G [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
D [auth A]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
TTC BindingDB:  1K4T Kd: 26.5 (nM) from 1 assay(s)
IC50: min: 21, max: 2.29e+4 (nM) from 13 assay(s)
EC50: min: 54, max: 71.3 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.269 (Depositor) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.093α = 90
b = 116.26β = 94.16
c = 75.217γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNXrefinement
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

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

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-11-15
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-10-30
    Changes: Structure summary