Structure of PDB 5hbj Chain A Binding Site BS01

Receptor Information
>5hbj Chain A (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKD
YALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFD
YAEHDLWHIIKFHRASKAVQLPRGMVKSLLYQILDGIHYLHANWVLHRDL
KPANILVMGEGPERGRVKIADMGFLFNSPLVTFWYRAPELLLGARHYTKA
IDIWAIGCIFAELLTSEPIFHCRQSNPYHHDQLDRIFNVMGFPADKDWED
IKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMD
PIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTE
Ligand information
Ligand ID5Y8
InChIInChI=1S/C21H23ClN6O/c1-27-16-3-2-13(10-14(16)11-26-27)15-12-25-19(23)17(22)18(15)28-8-5-21(6-9-28)4-7-24-20(21)29/h2-3,10-12H,4-9H2,1H3,(H2,23,25)(H,24,29)
InChIKeyVPJXPDLMACOGIZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4Cn1c2ccc(cc2cn1)c3cnc(c(c3N4CCC5(CCNC5=O)CC4)Cl)N
CACTVS 3.385Cn1ncc2cc(ccc12)c3cnc(N)c(Cl)c3N4CCC5(CCNC5=O)CC4
FormulaC21 H23 Cl N6 O
Name8-[2-azanyl-3-chloranyl-5-(1-methylindazol-5-yl)pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one
ChEMBLCHEMBL3798382
DrugBank
ZINC
PDB chain5hbj Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5hbj Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		V27 Y32 V35 A50 K52 I79 A100 L158 A172 D173 R356
Binding residue
(residue number reindexed from 1)		V29 Y34 V37 A52 K54 I81 A102 L156 A170 D171 R337
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.64,IC50=2.3nM
BindingDB: IC50=2.3nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 N181 T196
Catalytic site (residue number reindexed from 1) D149 K151 N154 D171 N177 T182
Enzyme Commision number 2.7.11.22: cyclin-dependent kinase.
2.7.11.23: [RNA-polymerase]-subunit kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5hbj, PDBe:5hbj, PDBj:5hbj
PDBsum5hbj
PubMed26796641
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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