Structure of PDB 5hvy Chain A Binding Site BS01

Receptor Information
>5hvy Chain A (length=335) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKMDYDFKVKLSSERERVEDLFEYEGCKVGGHVYKAKRKDGKDDKDYALK
QIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEH
DLWHIIKFHRASVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANIL
VMGEGPERGRVKIADMGFARLPVVVTFWYRAPELLLGARHYTKAIDIWAI
GCIFAELLTSEPIFHCRKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMP
EHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRI
TSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFL
Ligand information
Ligand ID66X
InChIInChI=1S/C22H28F3N7O2/c1-26-20-27-6-4-19(30-20)32-7-5-17(14-32)29-21(33)28-16-3-2-15(18(12-16)22(23,24)25)13-31-8-10-34-11-9-31/h2-4,6,12,17H,5,7-11,13-14H2,1H3,(H,26,27,30)(H2,28,29,33)/t17-/m0/s1
InChIKeyLVIYMOOJJGCMCP-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNc1nccc(n1)N2CC[C@@H](C2)NC(=O)Nc3ccc(CN4CCOCC4)c(c3)C(F)(F)F
ACDLabs 12.01C1C(CCN1c2ccnc(NC)n2)NC(Nc3cc(c(cc3)CN4CCOCC4)C(F)(F)F)=O
OpenEye OEToolkits 2.0.4CNc1nccc(n1)N2CC[C@@H](C2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)CN4CCOCC4
CACTVS 3.385CNc1nccc(n1)N2CC[CH](C2)NC(=O)Nc3ccc(CN4CCOCC4)c(c3)C(F)(F)F
OpenEye OEToolkits 2.0.4CNc1nccc(n1)N2CCC(C2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)CN4CCOCC4
FormulaC22 H28 F3 N7 O2
NameN-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea
ChEMBLCHEMBL4532382
DrugBank
ZINCZINC000584905269
PDB chain5hvy 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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PDB5hvy Design and Development of a Series of Potent and Selective Type II Inhibitors of CDK8.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		A50 E66 L69 I79 Y99 A100 L148 L158 A172 D173 M174
Binding residue
(residue number reindexed from 1)		A48 E64 L67 I77 Y97 A98 L140 L150 A164 D165 M166
Annotation score1
Binding affinityMOAD: ic50=17.4nM
PDBbind-CN: -logKd/Ki=7.76,IC50=17.4nM
BindingDB: IC50=>10000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 T196
Catalytic site (residue number reindexed from 1) D143 K145 N148 D165 T176
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:5hvy, PDBe:5hvy, PDBj:5hvy
PDBsum5hvy
PubMed27326333
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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