Structure of PDB 5idp Chain A Binding Site BS01

Receptor Information
>5idp 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]
KMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDY
ALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDY
AEHDLWHIIKFHRASKVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKP
ANILVMGEGPERGRVKIADMGFARLFNSPLKTFWYRAPELLLGARHYTKA
IDIWAIGCIFAELLTSEPIFHCRQETSNPYHHDQLDRIFNVMGFPADKDW
EDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLT
MDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL
Ligand information
Ligand ID6A6
InChIInChI=1S/C19H19FN4O/c20-14-7-4-12(5-8-14)17-3-1-2-10-24(17)19(25)13-6-9-16-15(11-13)18(21)23-22-16/h4-9,11,17H,1-3,10H2,(H3,21,22,23)/t17-/m0/s1
InChIKeyVXYMGUGNDZARSZ-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1n[nH]c2ccc(cc12)C(=O)N3CCCC[C@H]3c4ccc(F)cc4
OpenEye OEToolkits 2.0.4c1cc(ccc1C2CCCCN2C(=O)c3ccc4c(c3)c(n[nH]4)N)F
CACTVS 3.385Nc1n[nH]c2ccc(cc12)C(=O)N3CCCC[CH]3c4ccc(F)cc4
OpenEye OEToolkits 2.0.4c1cc(ccc1[C@@H]2CCCCN2C(=O)c3ccc4c(c3)c(n[nH]4)N)F
ACDLabs 12.01c4(ccc(C3N(C(c1ccc2c(c1)c(nn2)N)=O)CCCC3)cc4)F
FormulaC19 H19 F N4 O
Name(3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone
ChEMBLCHEMBL3984494
DrugBank
ZINCZINC000584904889
PDB chain5idp 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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PDB5idp Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		V27 Y32 V35 A50 F97 D98 A100 A155 L158 D173 R356
Binding residue
(residue number reindexed from 1)		V28 Y33 V36 A51 F98 D99 A101 A151 L154 D169 R339
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.35,IC50=45nM
BindingDB: IC50=800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 N181 T196
Catalytic site (residue number reindexed from 1) D147 K149 N152 D169 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
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Biological Process
External links
PDB RCSB:5idp, PDBe:5idp, PDBj:5idp
PDBsum5idp
PubMed27490956
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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