4WNP: ULK1

Structure of ULK1 bound to a potent inhibitor. Determined by X-ray diffraction at 1.88 Å resolution. Released 14 Jan 2015.

Method: X-ray diffraction
Resolution: 1.88 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,214
Mol. weight: 131.05 kDa
Ligands: 3RJ
Released: 14 Jan 2015

Explore 4WNP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WNP contains 52 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: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
β-strand	14-24	11	1
β-strand	29-35	7	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	151-153	3
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	249-258	10
α-helix	269-273	5
α-helix	276-278	3

Chain B: 12 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	78-83	6	5
β-strand	88-93	6	5
α-helix	94	1
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
β-strand	160-163	4	6
β-strand	170-171	2	7
β-strand	178	1	8
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	269-273	5

Chain C: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	9
β-strand	14-24	11	9
β-strand	29-35	7	9
β-strand	42-47	6	9
α-helix	50-52	3
α-helix	53-67	15
β-strand	75	1	10
β-strand	78-83	6	9
β-strand	88-93	6	9
β-strand	98-99	2	10
α-helix	100-107	8
α-helix	112-132	21
β-strand	134-135	2	11
α-helix	141-143	3
β-strand	144-147	4	10
α-helix	151-153	3
α-helix	156-158	3
β-strand	160-163	4	10
β-strand	170-171	2	11
β-strand	178	1	12
α-helix	185-187	3
α-helix	190-193	4
β-strand	198	1	12
α-helix	201-216	16
α-helix	226-235	10
α-helix	249-258	10
α-helix	269-273	5

Chain D: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	13
β-strand	14-24	11	13
β-strand	29-35	7	13
β-strand	42-47	6	13
α-helix	50-52	3
α-helix	53-67	15
β-strand	75	1	14
β-strand	78-83	6	13
β-strand	88-93	6	13
β-strand	99	1	14
α-helix	100-107	8
α-helix	112-132	21
β-strand	134-135	2	15
α-helix	141-143	3
β-strand	144-147	4	14
α-helix	156-158	3
β-strand	160-163	4	14
β-strand	170-171	2	15
β-strand	178	1	16
α-helix	185-187	3
α-helix	190-193	4
β-strand	198	1	16
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	287	Homo sapiens	O75385 (AlphaFold model)

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

>4WNP_1 Serine/threonine-protein kinase ULK1 (chains A, B, C, D)
GGGSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKS
QTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIR
LFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNM
MAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKN
KTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS

Ligands and cofactors

ID	Name	Formula	Copies
3RJ	N~2~-(1H-benzimidazol-6-yl)-N~4~-(5-cyclobutyl-1H-pyrazol-3-yl)quinazoline-2,4-…	C22 H20 N8	4

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

Primary citation

Structure of the Human Autophagy Initiating Kinase ULK1 in Complex with Potent Inhibitors. Lazarus, M.B., Novotny, C.J., Shokat, K.M. ACS Chem Biol (2015) 10:257-261. DOI 10.1021/cb500835z · PubMed

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
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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