Structure of PDB 5icp Chain A Binding Site BS01

Receptor Information
>5icp Chain A (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYA
LKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYA
EHDLWHIIKFHRASKLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANI
LVMGEGPERGRVKIADMGFARLFNSPLKVVTFWYRAPELLLGARHYTKAI
DIWAIGCIFAELLTSEPIFHCRQESNPYHHDQLDRIFNVMGFPADKDWED
IKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMD
PIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEE
Ligand information
Ligand ID69Z
InChIInChI=1S/C16H15ClN4OS/c1-10-18-9-14-21(10)19-15(23-14)16(22)20-8-2-3-13(20)11-4-6-12(17)7-5-11/h4-7,9,13H,2-3,8H2,1H3/t13-/m0/s1
InChIKeySAVNWXMDAMFANR-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4Cc1ncc2n1nc(s2)C(=O)N3CCCC3c4ccc(cc4)Cl
ACDLabs 12.01c1(ccc(cc1)C2CCCN2C(c3sc4n(n3)c(C)nc4)=O)Cl
OpenEye OEToolkits 2.0.4Cc1ncc2n1nc(s2)C(=O)N3CCC[C@H]3c4ccc(cc4)Cl
CACTVS 3.385Cc1ncc2sc(nn12)C(=O)N3CCC[CH]3c4ccc(Cl)cc4
CACTVS 3.385Cc1ncc2sc(nn12)C(=O)N3CCC[C@H]3c4ccc(Cl)cc4
FormulaC16 H15 Cl N4 O S
Name[(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](5-methylimidazo[5,1-b][1,3,4]thiadiazol-2-yl)methanone
ChEMBLCHEMBL3938208
DrugBank
ZINCZINC000210697593
PDB chain5icp Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5icp Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening.
Resolution2.18 Å
Binding residue
(original residue number in PDB)		V27 Y32 V35 A50 K52 F97 A100 L158 D173 R356
Binding residue
(residue number reindexed from 1)		V27 Y32 V35 A50 K52 F97 A100 L151 D166 R337
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.42,IC50=3.8nM
BindingDB: IC50=70nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 N181 T196
Catalytic site (residue number reindexed from 1) D144 K146 N149 D166 N174 T181
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:5icp, PDBe:5icp, PDBj:5icp
PDBsum5icp
PubMed27490956
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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