Citations in PubMed

Primary Citation PubMed: 21778401 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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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.

Publication Year: 2013


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 [40] ) was used as a template.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4538842

(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