Structure of PDB 3rgf Chain A Binding Site BS01

Receptor Information
>3rgf Chain A (length=321) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKMDYDFKVKLSSERERVEDLFEYEGCKVGHVYKAKRKDGKDDKDYALKQ
IEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHD
LWHIIKFHRASKLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVM
GEGPERGRVKIADMGFARVTFWYRAPELLLGARHYTKAIDIWAIGCIFAE
LLTSEPIFHCRQNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKD
FRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQD
PYFLEDPLPTSDVFAGCQIPY
Ligand information
Ligand IDBAX
InChIInChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
InChIKeyMLDQJTXFUGDVEO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c3nccc(Oc2ccc(NC(=O)Nc1ccc(Cl)c(c1)C(F)(F)F)cc2)c3)NC
OpenEye OEToolkits 1.5.0CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
CACTVS 3.341CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
FormulaC21 H16 Cl F3 N4 O3
Name4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE;
Sorafenib
ChEMBLCHEMBL1336
DrugBankDB00398
ZINCZINC000001493878
PDB chain3rgf Chain A Residue 465 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rgf The Structure of CDK8/CycC Implicates Specificity in the CDK/Cyclin Family and Reveals Interaction with a Deep Pocket Binder.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A50 K52 E66 L70 V78 I79 F97 Y99 A100 A172 D173 M174 F176
Binding residue
(residue number reindexed from 1)		A47 K49 E63 L67 V75 I76 F94 Y96 A97 A162 D163 M164 F166
Annotation score1
Binding affinityMOAD: ic50=0.13uM
BindingDB: Kd=310nM,IC50=1620nM
Enzymatic activity
Catalytic site (original residue number in PDB) D151 K153 N156 D173 T196
Catalytic site (residue number reindexed from 1) D141 K143 N146 D163 T170
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:3rgf, PDBe:3rgf, PDBj:3rgf
PDBsum3rgf
PubMed21806996
UniProtP49336|CDK8_HUMAN Cyclin-dependent kinase 8 (Gene Name=CDK8)

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