Primary Citation PubMed: 21778401
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Mapping small molecule binding data to structural domains.
(2012) BMC Bioinformatics 13 Suppl 17
PubMed: 23282026 | PubMedCentral: PMC3521243 | DOI: 10.1186/1471-2105-13-S17-S11
Examples were rendered using PDB files 1zdp, 3ee2, 3qx3, 1u3u, respectively.
Publication Year: 2012
Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide--a novel topoisomerase II inhibitor.
(2013) J Mol Model 19
PubMed: 23187686 | PubMedCentral: PMC3578725 | DOI: 10.1007/s00894-012-1679-6
Automated docking setup Docking was performed by means of the FlexX program [ 12 ] as implemented in LeadIT software package [ 13 ] using models of Topo II binding site complexed with AMP-PNP (PDB id ... ZXN [ 14 ]) and etoposide (PDB id 3QX3 [ 15 ]) as templates.
Mean values ± SD of three independent experiments performed in duplicate are presented Computational studies To examine the mode of inhibitory action of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride, 1 , docking simulations were performed with ATP-binding domain of hTopoIIα (PDB: 1ZXM) and DNA binding site of hTopoIIβ (PDB id: 3QX3) using the FlexX program, which has been shown to be reliable enough to carry out binding mode analysis of ligands in ATP binding pocket of hTopoIIα [ 31 ].
Publication Year: 2013
On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs.
(2013) Nucleic Acids Res 41
PubMed: 24038465 | PubMedCentral: PMC3905874 | DOI: 10.1093/nar/gkt828
All structures were solved by directly submitting the respective diffraction data sets to rigid body refinement using the drug-free structure of the hTop2β core -DNA-etoposide complex (PDBid: ... QX3) as the starting model.
The cytotoxicity of benzaldehyde nitrogen mustard-2-pyridine carboxylic acid hydrazone being involved in topoisomerase II? inhibition.
(2014) Biomed Res Int 2014
PubMed: 24995306 | PubMedCentral: PMC4066686 | DOI: 10.1155/2014/527042
Based on the recommended procedure, the ligand free type II topoisomerase derived from 3QX3 (PDB ID: 3QX3) was chosen as receptor, and the BNMPH was used as ligand.
Molecular Docking Studies The structure of human type II DNA topoisomerase with DNA and etoposide (3QX3) was obtained from RCSB Protein Data Bank [ 17 ].
Publication Year: 2014
Novel DNA topoisomerase II? inhibitors from combined ligand- and structure-based virtual screening.
(2014) PLoS One 9
PubMed: 25489853 | PubMedCentral: PMC4260913 | DOI: 10.1371/journal.pone.0114904
Homology modelling To generate homology models of human Top2α, the crystal structure of the ternary Top2β-DNA-etoposide complex (PDB code: 3QX3  ) was used as a template.
PubMed ID is not available.
Published in 2015
(C) conformations of the gate-DNA in the representative snapshot from simulation UD1 (hTopIIβ-cc), the crystal of drug-bound topoisomerase II (hTopIIβ-tc; PDB code 3QX3), the pre-cleav... ge complex of yeast topoisomerase II (yTopII-pcc; PDB code 2RGR), and topoisomerase IV with the ‘resealed’ DNA (sTopIV; PDB code 3KSB).
MATERIALS AND METHODS Molecular models and molecular dynamics simulations Crystal coordinates of the etoposide-stabilized (PDB code: 3QX3) and the eluted drug-free (PDB code: 4J3N) cleavage complexes of human topoisomerase IIβ were used.
( A ) RMSD between Cα atoms of WHD in the simulation with reference to the crystal of drug-bound complex (hTopIIβ-t.c.; 3QX3), the non-covalent complex of IIα isozyme (hTopIIα; 4FM9), topoisomerase IV with the ‘resealed’ DNA (sTopIV; 3KSB), and the cleavage complex of yeast enzyme (yTopII-c.c.
( A ) crystal structure of the drug-bound complex (3QX3; drug not shown).
Publication Year: 2015
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