9F32: ULK1 with a covalent compound GCL 99

Crystal structure of ULK1 with a covalent compound GCL 99. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Jan 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,967
Mol. weight: 32.51 kDa
Ligands: A1H9M
Released: 8 Jan 2025

Explore 9F32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F32 contains 10 α-helices and 10 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: 10 helices, 10 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	42-49	8	1
β-strand	75	1	2
β-strand	78-83	6	1
β-strand	87-93	7	1
β-strand	99	1	2
α-helix	100-107	8
α-helix	112-131	20
α-helix	141-143	3
β-strand	144-147	4	2
α-helix	159	1
β-strand	160-163	4	2
α-helix	190-193	4
α-helix	201-216	16
α-helix	226-235	10
α-helix	249-258	10
α-helix	269-273	5
α-helix	276-279	4

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>9F32_1 Serine/threonine-protein kinase ULK1 (chains A)
GSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQT
LLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLF
LQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMA
ATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKT
LVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS

Ligands and cofactors

ID	Name	Formula	Copies
A1H9M	N-[4-(1H-indazol-5-yl)phenyl]propanamide	C16 H15 N3 O	1

Primary citation

Probing the Protein Kinases' Cysteinome by Covalent Fragments. Wang, G., Seidler, N.J., Rohm, S. et al. Angew Chem Int Ed Engl (2025) 64:e202419736-e202419736. DOI 10.1002/anie.202419736 · 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
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
8P5J 2.16 Å, Kinase domain of mutant human ULK1 in complex with compound WZ4003

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