6BOD: TBK1

TBK1 in complex with ethyl ester analog of amlexanox. Determined by X-ray diffraction at 3.2 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,960
Mol. weight: 76.35 kDa
Ligands: E0P
Released: 26 Sept 2018

Explore 6BOD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BOD contains 24 α-helices and 22 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	1-3	3	1
β-strand	7-10	4	1
β-strand	14-17	4	2
β-strand	21-26	6	2
β-strand	27-28	2	1
β-strand	35-40	6	2
α-helix	53-60	8
β-strand	67	1	3
β-strand	70-75	6	2
β-strand	82-87	6	2
β-strand	93	1	3
α-helix	94-97	4
α-helix	101-103	3
α-helix	109-129	21
α-helix	138-140	3
β-strand	141-145	5	3
β-strand	151-155	5	3
α-helix	201-216	16
β-strand	221-222	2	4
α-helix	231-239	9
α-helix	241-242	2
β-strand	247-249	3	4
β-strand	258-260	3	4
α-helix	271-284	14
α-helix	289-291	3
α-helix	295-306	12
β-strand	308-315	8	5
β-strand	320-327	8	5
β-strand	331	1	6
α-helix	332-343	12
α-helix	347-349	3
β-strand	351-354	4	5
β-strand	357-359	3	5
β-strand	366	1	6
α-helix	367-369	3
α-helix	371-372	2
β-strand	379-382	4	5
α-helix	399-403	5
α-helix	408-479	72
α-helix	499-526	28
α-helix	536-538	3
α-helix	544-546	3
α-helix	548-571	24
α-helix	577-600	24
α-helix	601-606	6
α-helix	607-650	44

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase TBK1	A	protein	660	Homo sapiens	Q9UHD2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BOD_1 Serine/threonine-protein kinase TBK1 (chains A)
SNAMQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFE
VLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLR
DVVGGMNHLRENGIVHRDIKPGNIMRVIGEDGQSVYKLTDFGAARELEDDEQFVSLYGTE
EYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKI
ITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQ
FFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGR
RLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKA
ITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEK
TVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWA
HQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKA
MTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET

Ligands and cofactors

ID	Name	Formula	Copies
E0P	ethyl 2-amino-5-oxo-7-(propan-2-yl)-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxyl…	C18 H18 N2 O4	1

Primary citation

Carboxylic Acid Derivatives of Amlexanox Display Enhanced Potency toward TBK1 and IKKepsilonand Reveal Mechanisms for Selective Inhibition. Beyett, T.S., Gan, X., Reilly, S.M. et al. Mol Pharmacol (2018) 94:1210-1219. DOI 10.1124/mol.118.112185 · PubMed

Other PDB entries of the same protein (UniProt Q9UHD2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EP6 1.45 Å, The crystal structure of NAP1 in complex with TBK1
4EFO 1.77 Å, Crystal structure of the ubiquitin-like domain of human TBK1
4EUU 1.8 Å, Structure of BX-795 Complexed with Human TBK1 Kinase Domain Phosphorylated on Ser172
5EOF 2.05 Å, Crystal structure of OPTN NTD and TBK1 CTD complex
4IM0 2.4 Å, Structure of Tank-Binding Kinase 1
4IM2 2.5 Å, Structure of Tank-Binding Kinase 1
5EOA 2.5 Å, Crystal structure of OPTN E50K mutant and TBK1 complex
4EUT 2.6 Å, Structure of BX-795 Complexed with Unphosphorylated Human TBK1 Kinase-ULD Domain
4IWO 2.61 Å, Crystal structure and mechanism of activation of TBK1
6RSU 2.75 Å, TBK1 in complex with Inhibitor compound 35
4IWQ 3.0 Å, Crystal structure and mechanism of activation of TBK1
4IWP 3.06 Å, Crystal structure and mechanism of activation of TBK1

Browse structure collections

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