Structure of PDB 4im3 Chain A Binding Site BS01

Receptor Information
>4im3 Chain A (length=605) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNRPVDVQ
MREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPS
NAYGLPESEFLIVLRDVVGGMNHLRENGIVHRNIKPGNIMRVIGEDGQSV
YKLTDFGATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKP
SGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKC
WGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQ
TKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGL
IYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKG
IRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVAAELGEISDIH
TKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKL
QVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFT
DECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTN
ELQET
Ligand information
Ligand IDBX7
InChIInChI=1S/C23H26IN7O2S/c24-18-15-27-22(30-20(18)25-9-5-10-26-21(32)19-8-4-13-34-19)28-16-6-3-7-17(14-16)29-23(33)31-11-1-2-12-31/h3-4,6-8,13-15H,1-2,5,9-12H2,(H,26,32)(H,29,33)(H2,25,27,28,30)
InChIKeyVAVXGGRQQJZYBL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Ic1cnc(Nc2cccc(NC(=O)N3CCCC3)c2)nc1NCCCNC(=O)c4sccc4
ACDLabs 12.01O=C(NCCCNc1nc(ncc1I)Nc3cccc(NC(=O)N2CCCC2)c3)c4sccc4
OpenEye OEToolkits 1.7.6c1cc(cc(c1)NC(=O)N2CCCC2)Nc3ncc(c(n3)NCCCNC(=O)c4cccs4)I
FormulaC23 H26 I N7 O2 S
NameN-(3-{[5-iodo-4-({3-[(thiophen-2-ylcarbonyl)amino]propyl}amino)pyrimidin-2-yl]amino}phenyl)pyrrolidine-1-carboxamide
ChEMBLCHEMBL577784
DrugBank
ZINCZINC000003986669
PDB chain4im3 Chain A Residue 701 [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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PDB4im3 Structure and ubiquitination-dependent activation of TANK-binding kinase 1.
Resolution3.342 Å
Binding residue
(original residue number in PDB)		G18 A36 K38 M86 F88 C89 G92 T96 M142 T156 D157
Binding residue
(residue number reindexed from 1)		G20 A38 K40 M84 F86 C87 G90 T94 M140 T154 D155
Annotation score1
Binding affinityBindingDB: IC50=8.0nM,Kd=158nM
Enzymatic activity
Catalytic site (original residue number in PDB) N135 K137 N140 D157
Catalytic site (residue number reindexed from 1) N133 K135 N138 D155
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0019903 protein phosphatase binding
GO:0042802 identical protein binding
GO:0044024 histone H2AS1 kinase activity
GO:0051219 phosphoprotein binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0002218 activation of innate immune response
GO:0002753 cytoplasmic pattern recognition receptor signaling pathway
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006954 inflammatory response
GO:0007249 canonical NF-kappaB signal transduction
GO:0009615 response to virus
GO:0010468 regulation of gene expression
GO:0010508 positive regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0016236 macroautophagy
GO:0016239 positive regulation of macroautophagy
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0018107 peptidyl-threonine phosphorylation
GO:0032479 regulation of type I interferon production
GO:0032481 positive regulation of type I interferon production
GO:0032727 positive regulation of interferon-alpha production
GO:0032728 positive regulation of interferon-beta production
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0034142 toll-like receptor 4 signaling pathway
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0044565 dendritic cell proliferation
GO:0045087 innate immune response
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050830 defense response to Gram-positive bacterium
GO:0051607 defense response to virus
GO:0060337 type I interferon-mediated signaling pathway
GO:0060340 positive regulation of type I interferon-mediated signaling pathway
GO:0140374 antiviral innate immune response
GO:0140896 cGAS/STING signaling pathway
GO:1904262 negative regulation of TORC1 signaling
GO:1904263 positive regulation of TORC1 signaling
GO:1904417 positive regulation of xenophagy
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:1902554 serine/threonine protein kinase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4im3, PDBe:4im3, PDBj:4im3
PDBsum4im3
PubMed23453972
UniProtQ9UHD2|TBK1_HUMAN Serine/threonine-protein kinase TBK1 (Gene Name=TBK1)

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