Primary Citation PubMed: 11377199
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wwLigCSRre: a 3D ligand-based server for hit identification and optimization.
(2009) Nucleic Acids Res 37
PubMed: 19429687 | PubMedCentral: PMC2703967 | DOI: 10.1093/nar/gkp324
Example of scaffold hopping on CDK2 inhibitors Finally, to illustrate the scaffold hopping capacities of wwLigCSRre, we ran a quick run using the co-crystallized ligand of PDB structure 1E9H (a CDK2 i... hibitor) as the query on 47 diversified ligands including 9 CDK2, 9 coagulation factor Xa, 10 neuraminidase, 8 ribonuclease and 10 thymidine kinase inhibitors.
The three CDK2 hits, while having 3 different scaffolds, are superimposed onto the indirubin-based ligand of 1E9H.
1E9H ligand was used as the query ( a ) and three known CDK2 inhibitors were correctly detected and superimposed onto the query molecule ( b ), with respective z -scores of 3.353 ( c ), 2.708 ( d ) and 1.740 ( e ).
Publication Year: 2009
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
The 3 first CDK2 hits, for the 1E9H run, were obtained in a percentage level of subsetting inferior to 0.15% of the total test set (i.e within the top 60 of the ranked test set).
For CDK2 the query molecule was extracted from structure 1E9H and is based on an Indirubin scaffolds (two indole system rings), which is the only biindole-based ligand of the CDK2 subset.
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.
The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms.
(2011) Nucleic Acids Res 39
PubMed: 21036862 | PubMedCentral: PMC3013667 | DOI: 10.1093/nar/gkq1059
For instance, PDB entry 1E9H contains the sequence of cyclin A3, which has the chain architecture ‘(cyclin_N)_(cyclin_C)’.
For instance, the PFAM entry architecture of PDB entry 1E9H is ‘(cyclin_N)_(cyclin_C);(Pkinase)’.
Publication Year: 2011
High throughput screens yield small molecule inhibitors of Leishmania CRK3:CYC6 cyclin-dependent kinase.
(2011) PLoS Negl Trop Dis 5
PubMed: 21483720 | PubMedCentral: PMC3071374 | DOI: 10.1371/journal.pntd.0001033
The crystal structure of the human CDK2-CYCA complexed with the small molecule inhibitor indirubin-5-sulfonate (pdb code 1E9H) was used as the model template.
Novel Inverse Binding Mode of Indirubin Derivatives Yields Improved Selectivity for DYRK Kinases.
(2013) ACS Med Chem Lett 4
PubMed: 23336033 | PubMedCentral: PMC3545483 | DOI: 10.1021/ml300207a
11 − 17 Regardless of the notable selectivity of the various indirubin analogues, they all share a common interaction pattern with their target enzyme active site (for example, see PDB structu... es 1E9H, 2BHE, 1UV5, and 1UNH).
Publication Year: 2013
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.
Molecular dynamics study of the inhibitory effects of ChEMBL474807 on the enzymes GSK-3? and CDK-2.
(2015) J Mol Model 21
PubMed: 25754137 | PubMedCentral: PMC4353878 | DOI: 10.1007/s00894-015-2627-z
Fig. 1a–b The most important interactions observed between ChEMBL474807 and the active sites in the enzymes CDK-2 ( a ) and GSK-3β ( b ) Methods During the docking simulations, the cry... tal structures of CDK-2 (PDB ID: 1E9H) [ 25 ] and GSK-3β (PDB ID: 1Q41) were used [ 26 ], both of which were downloaded from the Brookhaven Protein Database (PDB).
Publication Year: 2015
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