Structure of PDB 5w84 Chain B Binding Site BS01

Receptor Information
>5w84 Chain B (length=264) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKDQEI
KVMAKCQHENLVELLGFSCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCK
IAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASTVMT
SRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQL
LLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRP
DIKKVQQLLQEMTA
Ligand information
Ligand ID9YY
InChIInChI=1S/C21H19N5O2/c22-21(28)16-12-24-19(10-18(16)23-11-13-4-2-1-3-5-13)25-15-6-7-17-14(8-15)9-20(27)26-17/h1-8,10,12H,9,11H2,(H2,22,28)(H,26,27)(H2,23,24,25)
InChIKeyMSYMSSQHTUWZDQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1ccc(cc1)CNc2cc(ncc2C(=O)N)Nc3ccc4c(c3)CC(=O)N4
ACDLabs 12.01c1(ccccc1)CNc2c(cnc(c2)Nc4cc3CC(=O)Nc3cc4)C(=O)N
CACTVS 3.385NC(=O)c1cnc(Nc2ccc3NC(=O)Cc3c2)cc1NCc4ccccc4
FormulaC21 H19 N5 O2
Name4-(benzylamino)-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyridine-3-carboxamide
ChEMBLCHEMBL4098698
DrugBank
ZINC
PDB chain5w84 Chain B Residue 4000 [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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PDB5w84 Discovery and structure-based design of 4,6-diaminonicotinamides as potent and selective IRAK4 inhibitors.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		M192 G193 E194 V200 V246 Y262 Y264 M265 G268 L318 D329
Binding residue
(residue number reindexed from 1)		M25 G26 E27 V33 V62 Y72 Y74 M75 G78 L128 D139
Annotation score1
Binding affinityBindingDB: IC50=360nM
Enzymatic activity
Catalytic site (original residue number in PDB) D311 K313 A315 N316 D329 T351
Catalytic site (residue number reindexed from 1) D121 K123 A125 N126 D139 T156
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007165 signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5w84, PDBe:5w84, PDBj:5w84
PDBsum5w84
PubMed28947151
UniProtQ9NWZ3|IRAK4_HUMAN Interleukin-1 receptor-associated kinase 4 (Gene Name=IRAK4)

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