9CE4: Serine/threonine-protein kinase Chk1

Structure of CHK1 10-pt. mutant complex with LRRK2 indazole inhibitor compound 6. Determined by X-ray diffraction at 1.31 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 1.31 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,401
Mol. weight: 31.78 kDa
Ligands: A1AV4
Released: 18 Sept 2024

Explore 9CE4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CE4 contains 14 α-helices and 18 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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
β-strand	9-16	8	1
β-strand	23-28	6	1
β-strand	34-40	7	1
α-helix	49-61	13
β-strand	67	1	2
α-helix	68-69	2
β-strand	70-76	7	1
β-strand	79-84	6	1
β-strand	91	1	2
α-helix	92-95	4
α-helix	96	1
β-strand	97	1	3
β-strand	101	1	3
α-helix	104-123	20
β-strand	126-127	2	4
α-helix	133-135	3
β-strand	136-138	3	2
β-strand	144-146	3	2
β-strand	153-154	2	4
β-strand	156-157	2	5
β-strand	160-161	2	5
β-strand	164	1	6
α-helix	171-173	3
α-helix	176-180	5
β-strand	184	1	6
α-helix	186-203	18
α-helix	216-222	7
α-helix	231-233	3
α-helix	236-245	10
α-helix	254-255	2
α-helix	256-259	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase Chk1	A	protein	268	Homo sapiens	O14757 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CE4_1 Serine/threonine-protein kinase Chk1 (chains A)
PFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLN
HENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHG
IGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRRE
FHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLH
KILVENPSARITIPDIKKDRWYNKPLKK

Ligands and cofactors

ID	Name	Formula	Copies
A1AV4	(1S,4r)-4-[(1P)-5-chloro-1-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-6-yl]-1-(oxeta…	C19 H23 Cl N5 O	1

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

Primary citation

Discovery and Optimization of N-Heteroaryl Indazole LRRK2 Inhibitors. Logan, K.M., Kaplan, W., Simov, V. et al. J Med Chem (2024) 67:16807-16819. DOI 10.1021/acs.jmedchem.4c01627 · PubMed

Other PDB entries of the same protein (UniProt O14757 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YEX 1.3 Å, Synthesis and evaluation of triazolones as checkpoint kinase 1 inhibitors
4HYI 1.4 Å, X-RAY Crystal structure of compound 40 bound to human chk1 kinase domain
3PA3 1.4 Å, X-ray crystal structure of compound 70 bound to human CHK1 kinase domain
5OQ5 1.4 Å, Structure of CHK1 8-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor
3OT3 1.44 Å, X-ray crystal structure of compound 22k bound to human Chk1 kinase domain
7SUF 1.48 Å, Structure of CHK1 10-pt. mutant complex with LRRK2 inhibitor 06
7SUG 1.48 Å, Structure of CHK1 10-pt. mutant complex with LRRK2 inhibitor 09
8E80 1.49 Å, Structure of LRRK2-CHK1 10-pt. mutant complex with heteroaryl-1H-indazole LRRK2…
5OPB 1.55 Å, Structure of CHK1 10-pt. mutant complex with indazole LRRK2 inhibitor
5OPU 1.55 Å, Structure of CHK1 10-pt. mutant complex with pyrrolopyridine LRRK2 inhibitor
8SIX 1.55 Å, Structure of Compound 13 bound to the CHK1 10-point mutant
3PA4 1.59 Å, X-ray crystal structure of compound 2a bound to human CHK1 kinase domain

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