Structure of PDB 5idn Chain A Binding Site BS01

Receptor Information
>5idn Chain A (length=336) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYA
LKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYA
EHDLWHIIKFHRASKANLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPA
NILVMGEGPERGRVKIADMGFARVTFWYRAPELLLGARHYTKAIDIWAIG
CIFAELLTSEPIFHCRQNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHS
TLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSE
QAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEE
Ligand information
Ligand ID6A7
InChIInChI=1S/C18H17ClN4O/c1-11-15-9-13(10-20-17(15)22-21-11)18(24)23-8-2-3-16(23)12-4-6-14(19)7-5-12/h4-7,9-10,16H,2-3,8H2,1H3,(H,20,21,22)/t16-/m0/s1
InChIKeyODRITQGYYWHQGM-INIZCTEOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1n[nH]c2ncc(cc12)C(=O)N3CCC[C@H]3c4ccc(Cl)cc4
OpenEye OEToolkits 2.0.4Cc1c2cc(cnc2[nH]n1)C(=O)N3CCCC3c4ccc(cc4)Cl
OpenEye OEToolkits 2.0.4Cc1c2cc(cnc2[nH]n1)C(=O)N3CCC[C@H]3c4ccc(cc4)Cl
CACTVS 3.385Cc1n[nH]c2ncc(cc12)C(=O)N3CCC[CH]3c4ccc(Cl)cc4
ACDLabs 12.01c1(Cl)ccc(cc1)C2N(CCC2)C(c4cc3c(C)nnc3nc4)=O
FormulaC18 H17 Cl N4 O
Name[(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone
ChEMBLCHEMBL3903492
DrugBank
ZINC
PDB chain5idn 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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PDB5idn Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		V27 Y32 A50 K52 F97 A100 L158 R356
Binding residue
(residue number reindexed from 1)		V27 Y32 A50 K52 F97 A100 L153 R329
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.59,IC50=2.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 T196
Catalytic site (residue number reindexed from 1) D146 K148 N151 D168 T175
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

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5idn, PDBe:5idn, PDBj:5idn
PDBsum5idn
PubMed27490956
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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