8P5I: Kinase domain of mutant human ULK1

Kinase domain of mutant human ULK1 in complex with compound XMD-17-51. Determined by X-ray diffraction at 1.83 Å resolution. Released 5 Jun 2024.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,079
Mol. weight: 130.55 kDa
Ligands: MG, WYX
Released: 5 Jun 2024

Explore 8P5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P5I contains 51 α-helices and 56 β-strands across 4 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: 12 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	88-92	5	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
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	249-258	10
α-helix	269-273	5
α-helix	276-278	3

Chains B and C: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	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	88-93	6	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
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
α-helix	276-278	3

Chain D: 13 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	12
β-strand	78-83	6	1
β-strand	88-93	6	1
β-strand	99	1	12
α-helix	100-107	8
α-helix	112-132	21
β-strand	134-135	2	13
α-helix	141-143	3
β-strand	144-147	4	12
α-helix	156-158	3
β-strand	160-163	4	12
β-strand	170-171	2	13
β-strand	178	1	14
α-helix	185-187	3
α-helix	190-193	4
β-strand	198	1	14
α-helix	201-216	16
α-helix	226-235	10
α-helix	249-258	10
α-helix	269-273	5
α-helix	276-278	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase ULK1	A, B, C, D	protein	284	Homo sapiens	O75385 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8P5I_1 Serine/threonine-protein kinase ULK1 (chains A, B, C, D)
SMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQTL
LGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFL
QQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAA
TLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTL
VPTIPAATSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
WYX	5,11-dimethyl-2-[(1-piperidin-4-ylpyrazol-4-yl)amino]pyrimido[4,5-b][1,4]benzod…	C21 H24 N8 O	4

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

Primary citation

Crystal structures of ULK1 in complex with KCGS compounds. Battista, T., Semrau, M.S., Lolli, G. 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
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
9SE8 2.0 Å, Crystal structure of ULK1 in complex with inhibitor SBP-5147
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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