Structure of PDB 8dks Chain A Binding Site BS01

Receptor Information
>8dks Chain A (length=283) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKK
LATTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGS
LLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILL
DEAFTAKISDFGLARASVMSRIVGTTAYMAPEALRGEITPKSDIYSFGVV
LLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSV
EAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTA
Ligand information
Ligand IDSO9
InChIInChI=1S/C25H26N6O2S/c26-22(32)19-14-6-7-15(12-14)20(19)29-23-21-18(8-11-34-21)28-25(30-23)27-17-5-3-4-16(13-17)24(33)31-9-1-2-10-31/h3-8,11,13-15,19-20H,1-2,9-10,12H2,(H2,26,32)(H2,27,28,29,30)/t14-,15+,19+,20-/m1/s1
InChIKeyALXDIYXXVBXYGK-VVVONTASSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(cc(c1)Nc2nc3ccsc3c(n2)N[C@@H]4[C@@H]5C[C@H]([C@@H]4C(=O)N)C=C5)C(=O)N6CCCC6
CACTVS 3.385NC(=O)[C@H]1[C@H]2C[C@H](C=C2)[C@H]1Nc3nc(Nc4cccc(c4)C(=O)N5CCCC5)nc6ccsc36
OpenEye OEToolkits 2.0.7c1cc(cc(c1)Nc2nc3ccsc3c(n2)NC4C5CC(C4C(=O)N)C=C5)C(=O)N6CCCC6
CACTVS 3.385NC(=O)[CH]1[CH]2C[CH](C=C2)[CH]1Nc3nc(Nc4cccc(c4)C(=O)N5CCCC5)nc6ccsc36
ACDLabs 12.01NC(=O)C1C2C=CC(C2)C1Nc1nc(nc2ccsc12)Nc1cc(ccc1)C(=O)N1CCCC1
FormulaC25 H26 N6 O2 S
Name(1S,2S,3R,4R)-3-({2-[3-(pyrrolidine-1-carbonyl)anilino]thieno[3,2-d]pyrimidin-4-yl}amino)bicyclo[2.2.1]hept-5-ene-2-carboxamide
ChEMBLCHEMBL5185144
DrugBank
ZINC
PDB chain8dks 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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PDB8dks Bicyclic pyrimidine compounds as potent IRAK4 inhibitors.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		M192 A211 Y262 Y264 M265 P266 G268 R273 A315 L318 D329
Binding residue
(residue number reindexed from 1)		M28 A47 Y93 Y95 M96 P97 G99 R104 A146 L149 D160
Annotation score1
Enzymatic activity
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:0005149 interleukin-1 receptor binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019901 protein kinase binding
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0002224 toll-like receptor signaling pathway
GO:0002446 neutrophil mediated immunity
GO:0002755 MyD88-dependent toll-like receptor signaling pathway
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0007165 signal transduction
GO:0007254 JNK cascade
GO:0008063 Toll signaling pathway
GO:0016310 phosphorylation
GO:0019221 cytokine-mediated signaling pathway
GO:0031349 positive regulation of defense response
GO:0034142 toll-like receptor 4 signaling pathway
GO:0034162 toll-like receptor 9 signaling pathway
GO:0035556 intracellular signal transduction
GO:0038172 interleukin-33-mediated signaling pathway
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0045087 innate immune response
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0070498 interleukin-1-mediated signaling pathway
GO:0071222 cellular response to lipopolysaccharide
GO:1990266 neutrophil migration
Cellular Component
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0019897 extrinsic component of plasma membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dks, PDBe:8dks, PDBj:8dks
PDBsum8dks
PubMed35863718
UniProtQ9NWZ3|IRAK4_HUMAN Interleukin-1 receptor-associated kinase 4 (Gene Name=IRAK4)

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