9SE8: ULK1

Crystal structure of ULK1 in complex with inhibitor SBP-5147. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Aug 2026.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,868
Mol. weight: 67.74 kDa
Ligands: A1JNH
Released: 26 Aug 2026

Explore 9SE8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SE8 contains 29 α-helices and 28 β-strands across 2 chains. 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: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
β-strand	14-25	12	1
β-strand	28-35	8	1
β-strand	42-47	6	1
α-helix	50-52	3
α-helix	53-67	15
β-strand	75	1	2
β-strand	78-83	6	1
β-strand	88-93	6	1
β-strand	99	1	2
α-helix	100-107	8
α-helix	112-132	21
β-strand	134-135	2	3
α-helix	141-143	3
β-strand	144-147	4	2
α-helix	156-158	3
β-strand	160-163	4	2
β-strand	170-171	2	3
β-strand	178	1	4
α-helix	185-187	3
α-helix	190-193	4
β-strand	198	1	4
α-helix	201-216	16
α-helix	226-235	10
α-helix	241-244	4
α-helix	249-258	10
α-helix	263-265	3
α-helix	269-273	5
α-helix	276-278	3

Chain B: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	5
β-strand	14-25	12	5
β-strand	28-35	8	5
β-strand	42-47	6	5
α-helix	50-52	3
α-helix	53-67	15
β-strand	75	1	6
β-strand	78-84	7	5
β-strand	87-93	7	5
β-strand	99	1	6
α-helix	100-107	8
α-helix	112-132	21
β-strand	134-135	2	7
α-helix	141-143	3
β-strand	144-147	4	6
α-helix	156-158	3
α-helix	159	1
β-strand	160-163	4	6
β-strand	170-171	2	7
β-strand	178	1	8
α-helix	185-187	3
α-helix	190-193	4
β-strand	198	1	8
α-helix	201-216	16
α-helix	226-235	10
α-helix	249-258	10
α-helix	263-265	3
α-helix	269-273	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase ULK1	A, B	protein	285	Homo sapiens	O75385 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9SE8_1 Serine/threonine-protein kinase ULK1 (chains A, B)
GSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQT
LLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLF
LQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMA
ATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKT
LVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS

Ligands and cofactors

ID	Name	Formula	Copies
A1JNH	~{N}4-cyclopropyl-~{N}2-(1,2,3,4-tetrahydroisoquinolin-6-yl)-5-(trifluoromethyl…	C17 H18 F3 N5	2

Water and common crystallization additives (EDO, GOL, SO4) are not listed.

Primary citation

Crystal structure of ULK1 in complex with inhibitor SBP-5147. Chaikuad, A., Layng, F.I.A.L., Ren, H. et al. To be published.

Other PDB entries of the same protein (UniProt O75385 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HYO 1.07 Å, Structure of ULK1 LIR motif bound to GABARAP
4WNO 1.56 Å, Structure of ULK1 bound to an inhibitor
6MNH 1.73 Å, ULK1 Unc-51 like autophagy activating kinase in complex with inhibitor BTC
5CI7 1.74 Å, Structure of ULK1 bound to a selective inhibitor
6QAS 1.75 Å, Crystal structure of ULK1 in complexed with PF-03814735
8P5I 1.83 Å, Kinase domain of mutant human ULK1 in complex with compound XMD-17-51
8P5L 1.84 Å, Kinase domain of mutant human ULK1 in complex with compound MRT67307
4WNP 1.88 Å, Structure of ULK1 bound to a potent inhibitor
8P5H 1.94 Å, Kinase domain of mutant human ULK1 in complex with compound CCT241533
8P5G 2.02 Å, Kinase domain of wild type human ULK1 in complex with compound CCT241533
9F32 2.1 Å, Crystal structure of ULK1 with a covalent compound GCL 99
8P5J 2.16 Å, Kinase domain of mutant human ULK1 in complex with compound WZ4003

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