Primary Citation PubMed: 11141566
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MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.
(2008) BMC Bioinformatics 9
PubMed: 18402678 | PubMedCentral: PMC2373571 | DOI: 10.1186/1471-2105-9-184
Crystal structures of estrogen receptor (ER, PDB code 3ert , resolution 1.90 Å), thymidine kinase (TK, PDB code 1kim , resolution 2.14 Å), coagulation factor X (FX, PDB code 1f0r , res... lution 2.10 Å), ribonuclease A (RNAse, PDB code 1afk , resolution 1.70 Å), neuraminidase (NA, PDB code 1b9s , resolution 2.50 Å), CDK2 (CDK, PDB code 1fvv , resolution 2.80 Å), and carboxypeptidase A (CBXpe, PDB code 1hdq , resolution 2.30 Å) were selected for the VLS experiments.
Publication Year: 2008
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
(2009) BMC Bioinformatics 10
PubMed: 19671127 | PubMedCentral: PMC2739202 | DOI: 10.1186/1471-2105-10-245
LigCSRre managed however to undertake some scaffolds hopping (e.g between 1E9H and 1FVV ligands), and other examples of scaffolds hopping could be cited like between 1OGU and 1H1S ligands.
Publication Year: 2009
High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations.
(2009) PLoS Comput Biol 5
PubMed: 19816553 | PubMedCentral: PMC2746282 | DOI: 10.1371/journal.pcbi.1000528
The left figure indicates the binding pocket in the CDK2-Oxindole inhibitor complex (PDB Id: 1FVV).
These structures with crystallographic resolutions of less than 3.0 Å, were retrieved from the Protein Data Bank (PDB) because the conformations of residues in the binding pocket affect the molecular docking results (PDB Id: 1C5S (trypsin)  , 1HWR (HIV PR)  , 1E66 (AChE)  , and 1FVV (CDK2)  ).
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities.
(2011) Nucleic Acids Res 39
PubMed: 21051336 | PubMedCentral: PMC3013767 | DOI: 10.1093/nar/gkq878
Case study 1: identifying cyclin dependent kinases inhibitors As a test for the pharmacaphore searching routine we used the eight available structures of CDK complexes stored in the PDBbind database (... 27 ) with PDB codes 1AQ1, 1DI8, 1DM2, 1E1V, 1E1X, 1FVV, 1UNH and 2A4L.
Publication Year: 2011
idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach.
(2012) Nucleic Acids Res 40
PubMed: 22649057 | PubMedCentral: PMC3394295 | DOI: 10.1093/nar/gks496
The predicted best targets are as follows: CDK2 (PDB ID: 1FVV, predicted Ki : 51.7 nM); CDK5 (PDB ID: 1UNH, predicted Ki : 71.2 nM); GSK-3β (PDB ID: 1Q41, predicted Ki : 63.3... 02009;nM); PDK1 (PDB ID: 2PE1, predicted Ki : 96.5 nM).
Publication Year: 2012
ReFlexIn: a flexible receptor protein-ligand docking scheme evaluated on HIV-1 protease.
(2012) PLoS One 7
PubMed: 23110159 | PubMedCentral: PMC3480487 | DOI: 10.1371/journal.pone.0048008
The last three non-binders correspond to ligands that bind to protein kinases (ligands from pdb ID's 1FMO, 1FVV, and 1JSV).
A structure-guided approach for protein pocket modeling and affinity prediction.
(2013) J Comput Aided Mol Des 27
PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9
PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.
Publication Year: 2013
PubMed ID is not available.
Published in 2015
Figure 6 shows a predicted pose for the 2XNB ligand (A), along with a depiction of its surface shape and electrostatic similarity to the bound pose of the ligand of 1FVV (B).
Publication Year: 2015
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