9QB5: AP2-associated protein kinase 1

AP2-associated protein kinase 1 (AAK1) bound to CKJB68. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Apr 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,014
Mol. weight: 73.09 kDa
Ligands: F7I
Released: 9 Apr 2025

Explore 9QB5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QB5 contains 29 α-helices and 32 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	1
β-strand	44-55	12	1
β-strand	58-65	8	1
β-strand	70-78	9	1
α-helix	81-97	17
β-strand	103	1	2
α-helix	104-105	2
β-strand	106-115	10	1
β-strand	119-127	9	1
β-strand	132-133	2	2
α-helix	134-139	6
α-helix	148-166	19
β-strand	173	1	3
α-helix	179-181	3
β-strand	182-184	3	2
β-strand	190-192	3	2
β-strand	199	1	3
β-strand	203	1	4
α-helix	205-208	4
α-helix	210-220	11
α-helix	223-225	3
α-helix	228-231	4
β-strand	239	1	4
α-helix	242-257	16
α-helix	266-271	6
β-strand	276	1	5
α-helix	284-293	10
α-helix	304-315	12
α-helix	333-337	5
β-strand	338	1	5
α-helix	339-341	3

Chain B: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	38-41	4	6
β-strand	44-55	12	6
β-strand	58-65	8	6
β-strand	70-78	9	6
α-helix	81-97	17
β-strand	103	1	7
α-helix	104-105	2
β-strand	106-115	10	6
β-strand	119-127	9	6
β-strand	132-133	2	7
α-helix	134-139	6
α-helix	148-166	19
β-strand	173	1	8
α-helix	179-181	3
β-strand	182-184	3	7
β-strand	190-192	3	7
β-strand	199	1	8
β-strand	203	1	9
α-helix	205-208	4
α-helix	210-220	11
α-helix	223-225	3
α-helix	228-231	4
β-strand	239	1	9
α-helix	242-257	16
α-helix	266-271	6
β-strand	275-276	2	10
α-helix	284-293	10
α-helix	304-315	12
α-helix	327-330	4
β-strand	337-338	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP2-associated protein kinase 1	A, B	protein	318	Homo sapiens	Q2M2I8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9QB5_1 AP2-associated protein kinase 1 (chains A, B)
MGLGSGYIGRVFGIGRQQVTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVC
KREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVVNLMNQRLQTGFT
ENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQT
EGVNAVEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQV
AICDGNFTIPDNSRYSQDMHCLIRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNS
PIPAKLPEPVKASEAAAK

Ligands and cofactors

ID	Name	Formula	Copies
F7I	~{N}-(phenylmethyl)-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{…	C24 H23 N5 O3	2

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

Primary citation

Development of pyrazolo[1,5-a]pyrimidine based macrocyclic kinase inhibitors targeting AAK1. Mensing, T.E., Kurz, C.G., Amrhein, J.A. et al. Eur J Med Chem (2025) 299:118076-118076. DOI 10.1016/j.ejmech.2025.118076 · PubMed

Other PDB entries of the same protein (UniProt Q2M2I8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6S 1.0 Å, PDZ domain in complex with the peptide from AP2-associated protein kinase 1
9F8T 1.71 Å, Clathrin terminal domain complexed with C-terminus of AAK1L
5TE0 1.9 Å, Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120
4WSQ 1.95 Å, Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small…
5L4Q 1.97 Å, Crystal Structure of Adaptor Protein 2 Associated Kinase 1 (AAK1) in Complex with LKB1…
8GMD 2.2 Å, CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH…
8GMC 2.5 Å, CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH…

Browse structure collections

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