Structure of PDB 4f6w Chain A Binding Site BS01

Receptor Information
>4f6w Chain A (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYA
LKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYA
EHDLWHIIKFHRASKVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPA
NILVMGEGPERGRVKIADMGFATFWYRAPELLLGARHYTKAIDIWAIGCI
FAELLTSEPIFHCRQNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTL
MKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQA
MQDPYFLEDPLPTSDVFAGCQIPYPKREFL
Ligand information
Ligand ID0SS
InChIInChI=1S/C36H49N9O2/c1-25-9-13-27(14-10-25)44-31(23-29(40-44)35(3,4)5)38-33(46)37-17-18-42-19-21-43(22-20-42)34(47)39-32-24-30(36(6,7)8)41-45(32)28-15-11-26(2)12-16-28/h9-16,23-24H,17-22H2,1-8H3,(H,39,47)(H2,37,38,46)
InChIKeyDWTWTHMDBSOYDZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1ccc(cc1)n2nc(cc2NC(=O)NCCN3CCN(CC3)C(=O)Nc4cc(nn4c5ccc(C)cc5)C(C)(C)C)C(C)(C)C
OpenEye OEToolkits 1.7.6Cc1ccc(cc1)n2c(cc(n2)C(C)(C)C)NC(=O)NCCN3CCN(CC3)C(=O)Nc4cc(nn4c5ccc(cc5)C)C(C)(C)C
ACDLabs 12.01O=C(Nc2cc(nn2c1ccc(cc1)C)C(C)(C)C)NCCN5CCN(C(=O)Nc4cc(nn4c3ccc(cc3)C)C(C)(C)C)CC5
FormulaC36 H49 N9 O2
NameN-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide
ChEMBLCHEMBL3401551
DrugBank
ZINCZINC000098207864
PDB chain4f6w Chain A Residue 501 [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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PDB4f6w Structure-kinetic relationship study of CDK8/CycC specific compounds.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		V27 Y32 S62 E66 F97 W105 A172 D173 M174 R356
Binding residue
(residue number reindexed from 1)		V27 Y32 S62 E66 F97 W105 A167 D168 M169 R327
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.52,Kd=0.03uM
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 T173
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:4f6w, PDBe:4f6w, PDBj:4f6w
PDBsum4f6w
PubMed23630251
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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