Primary Citation PubMed: 9030780
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Prediction of specificity-determining residues for small-molecule kinase inhibitors.
(2008) BMC Bioinformatics 9
PubMed: 19032760 | PubMedCentral: PMC2655090 | DOI: 10.1186/1471-2105-9-491
The 3D structure of CDK2 (PDB 2A4L , wire rendering with grey carbons) was superposed onto the structure of HCK (hidden) in complex with PP1 (PDB 1QCF , ball and stick rendering with green carbons).
The 3D structure of CDK2 (PDB 2A4L , wire rendering with grey carbons) was superposed onto the structure of MK2 (hidden) in complex with PHA-00781089 (PDB 2P3G , ball and stick rendering with green carbons).
The 3D structure of p38 (PDB 2GTM , wire rendering with grey carbons) was superposed onto the structure of CDK2 (hidden) in complex with Roscovitine (PDB 2A4L , ball and stick rendering with green carbons).
Table 1 S-Filter predictions Compound Primary target PDB Predictions FN FP TN TP Total SB-203580 p38 1A9U Leu 104 Thr 106 0 0 14 2 16 PHA-00781089 MK2 2P3G Cys 140 Gly 143 0 1 18 1 20 Roscovitine CDK2 2A4L Val 64 Leu 83 Ala 144 0 2 20 1 23 PP1 SRC/HCK 1QCF Thr 338 Gly 344 0 1 18 1 20 OSI-774 EGFR 1M17 Thr 766 Cys 773 0 1 19 1 21 GW-572016 EGFR 1XKK Cys 775 2 0 23 1 26 Fasudil ROCK1 2ESM Val 137 Met 153 Ala 215 1 2 14 1 17 Predicted specificity determinants are shown for each compound and are either designated as false positives (FP) or true positives (TP).
Publication Year: 2008
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
Identification and structural-functional analysis of cyclin-dependent kinases of the cattle tick Rhipicephalus (Boophilus) microplus.
(2013) PLoS One 8
PubMed: 24146826 | PubMedCentral: PMC3795742 | DOI: 10.1371/journal.pone.0076128
When this in silico analysis was compared with experimental observations that show the binding of roscovitine to human CDK2 (PDB ID: 2A4L;  , for example, the putative ATP binding sites of our 3D ... odels adopt a more closed conformation, and impairs the interaction with other proteins ( Figure S7 ).
Publication Year: 2013
PubMed ID is not available.
Published in 2015
The cyan and fuchsia patterns indicate the monomeric CDK2 (coordinates 2A4L) and the phosphorylated CDK2/cyclin A dimer (3DDQ) in a complex with roscovitine, respectively.
Panel ( A ) displays the competitive binding site of the monomer CDK2 with inhibitor roscovitine (coordinates 2A4L); the detailed information of amino acids in this cavity is shown in panel ( B ).
Publication Year: 2015
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