Structure of PDB 6bny Chain A Binding Site BS01

Receptor Information
>6bny Chain A (length=609) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLDVQM
REFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSN
AYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRVIGEDGQSVY
KLTDFGTEEYLHPDMYEVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVM
YKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANI
LEADQEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATI
FHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSR
EPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLL
YQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVELGEI
SDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRN
VEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAM
THFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ
EYTNELQET
Ligand information
Ligand IDE0M
InChIInChI=1S/C16H14N6O2/c1-7(2)8-3-4-12-9(5-8)13(23)10-6-11(15-19-21-22-20-15)14(17)18-16(10)24-12/h3-7H,1-2H3,(H2,17,18)(H,19,20,21,22)
InChIKeyYHCFWEQYIPEHCK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC(C)c4ccc1c(C(c2c(O1)nc(c(c2)c3nnnn3)N)=O)c4
CACTVS 3.385CC(C)c1ccc2Oc3nc(N)c(cc3C(=O)c2c1)c4[nH]nnn4
OpenEye OEToolkits 2.0.6CC(C)c1ccc2c(c1)C(=O)c3cc(c(nc3O2)N)c4[nH]nnn4
FormulaC16 H14 N6 O2
Name2-amino-7-(propan-2-yl)-3-(1H-tetrazol-5-yl)-5H-[1]benzopyrano[2,3-b]pyridin-5-one
ChEMBLCHEMBL153809
DrugBank
ZINCZINC000027636103
PDB chain6bny Chain A Residue 801 [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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PDB6bny Carboxylic Acid Derivatives of Amlexanox Display Enhanced Potency toward TBK1 and IKKepsilonand Reveal Mechanisms for Selective Inhibition.
Resolution3.341 Å
Binding residue
(original residue number in PDB)		L15 A36 M86 E87 F88 C89 G92 M142 T156
Binding residue
(residue number reindexed from 1)		L15 A36 M83 E84 F85 C86 G89 M139 T153
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.40,Kd=0.4uM
BindingDB: IC50=180nM
Enzymatic activity
Catalytic site (original residue number in PDB) D135 K137 N140 D157 T176
Catalytic site (residue number reindexed from 1) D132 K134 N137 D154 T157
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:6bny, PDBe:6bny, PDBj:6bny
PDBsum6bny
PubMed30082428
UniProtQ9UHD2|TBK1_HUMAN Serine/threonine-protein kinase TBK1 (Gene Name=TBK1)

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