Structure of PDB 5w5v Chain A Binding Site BS01

Receptor Information
>5w5v Chain A (length=599) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQSTSNHLWLLSDILTANVFRGRHKKTGDLFAIKVFVDVQMREFEVLKKL
NHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEF
LIVLRDVVGGMNHLRENGIVHRDIKPGNIMRVIGEDGQSVYKLTDFGEEY
LHPDMYERATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGK
PSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILDQEKCW
GFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQT
KIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLI
YEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGI
RWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVEISDIHTKLLRL
SSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNC
MTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKK
YEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET
Ligand information
Ligand IDANW
InChIInChI=1S/C16H14N2O4/c1-7(2)8-3-4-12-9(5-8)13(19)10-6-11(16(20)21)14(17)18-15(10)22-12/h3-7H,1-2H3,(H2,17,18)(H,20,21)
InChIKeySGRYPYWGNKJSDL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C)c1ccc2c(c1)C(=O)c3cc(c(nc3O2)N)C(=O)O
CACTVS 3.352CC(C)c1ccc2Oc3nc(N)c(cc3C(=O)c2c1)C(O)=O
ACDLabs 11.02O=C(O)c1cc2C(=O)c3cc(ccc3Oc2nc1N)C(C)C
FormulaC16 H14 N2 O4
Name2-amino-7-(1-methylethyl)-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid
ChEMBLCHEMBL1096
DrugBankDB01025
ZINCZINC000000000928
PDB chain5w5v 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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PDB5w5v Carboxylic Acid Derivatives of Amlexanox Display Enhanced Potency toward TBK1 and IKKepsilonand Reveal Mechanisms for Selective Inhibition.
Resolution3.645 Å
Binding residue
(original residue number in PDB)		E87 F88 C89 G92 T96 M142
Binding residue
(residue number reindexed from 1)		E75 F76 C77 G80 T84 M130
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.10,Kd=0.8uM
BindingDB: IC50=851nM
Enzymatic activity
Catalytic site (original residue number in PDB) D135 K137 N140 D157
Catalytic site (residue number reindexed from 1) D123 K125 N128 D145
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:5w5v, PDBe:5w5v, PDBj:5w5v
PDBsum5w5v
PubMed30082428
UniProtQ9UHD2|TBK1_HUMAN Serine/threonine-protein kinase TBK1 (Gene Name=TBK1)

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