Structure of PDB 6bod Chain A

Receptor sequence

>6bodA (length=610) Species: 9606 (Homo sapiens) [Search protein sequence]

AMQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNVQMREFEV
LKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLP
ESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRVIGEDGQSVYKLTDF
GAARETEEYLHPDMYERATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKE
VMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLA
NILEADQEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTA
TIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVV
SREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL
LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVE
ISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDR
NVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKA
MTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKY
QEYTNELQET

3D structure

PDB

6bod Carboxylic Acid Derivatives of Amlexanox Display Enhanced Potency toward TBK1 and IKKepsilonand Reveal Mechanisms for Selective Inhibition.

Chain

Resolution

3.197 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	D135 K137 N140 D157 T176
Catalytic site (residue number reindexed from 1)	D127 K129 N132 D149 T156
Enzyme Commision number	2.7.11.1: non-specific serine/threonine protein kinase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	E0P	A	L15 C89 M142 T156 D157	L16 C81 M134 T148 D149	PDBbind-CN: -logKd/Ki=4.26,Kd=55uM BindingDB: IC50=123000nM

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:6bod, PDBe:6bod, PDBj:6bod
PDBsum	6bod
PubMed	30082428
UniProt	Q9UHD2\|TBK1_HUMAN Serine/threonine-protein kinase TBK1 (Gene Name=TBK1)

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