9D50: PAK1

Structure of PAK1 in complex with compound 24. Determined by X-ray diffraction at 1.9 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,592
Mol. weight: 67.24 kDa
Ligands: A1A2T
Released: 2 Apr 2025

Explore 9D50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D50 contains 39 α-helices and 22 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: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	251-260	10
α-helix	266-269	4
β-strand	270-279	10	1
β-strand	282-289	8	1
β-strand	295-302	8	1
α-helix	303-305	3
α-helix	310-321	12
β-strand	327	1	2
α-helix	328-329	2
β-strand	330-336	7	1
β-strand	339-345	7	1
β-strand	350-351	2	2
α-helix	352-358	7
α-helix	363-382	20
β-strand	385-386	2	3
α-helix	392-394	3
β-strand	395-397	3	2
β-strand	403-405	3	2
β-strand	412-413	2	3
β-strand	421	1	4
α-helix	428-430	3
α-helix	433-436	4
β-strand	441	1	4
α-helix	444-459	16
α-helix	469-479	11
α-helix	482-484	3
α-helix	487-489	3
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-540	10

Chain B: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	254-260	7
α-helix	266-269	4
β-strand	270-278	9	5
β-strand	283-289	7	5
β-strand	295-302	8	5
α-helix	312-321	10
β-strand	327	1	6
β-strand	330-336	7	5
β-strand	339-345	7	5
β-strand	351	1	6
α-helix	352-358	7
α-helix	363-382	20
α-helix	392-394	3
β-strand	395-397	3	6
β-strand	403-405	3	6
α-helix	433-436	4
α-helix	445-459	15
α-helix	469-479	11
α-helix	482-484	3
α-helix	487-489	3
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-540	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PAK 1	A, B	protein	296	Homo sapiens	Q13153 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9D50_1 Serine/threonine-protein kinase PAK 1 (chains A, B)
DEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKK
ELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAV
CRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPY
WMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEK
LSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNH

Ligands and cofactors

ID	Name	Formula	Copies
A1A2T	3-cyano-N-[3-({6-[(5-cyclopropyl-1,3-thiazol-2-yl)amino]pyrazin-2-yl}amino)bicy…	C20 H22 N8 O S	2

Primary citation

Identification of a p21-activated kinase 1 (PAK1) inhibitor with 10-fold selectivity against PAK2. Johns, D.M., Olejniczak, J., Babbar, A. et al. Bioorg Med Chem Lett (2025) 127:130307-130307. DOI 10.1016/j.bmcl.2025.130307 · PubMed

Other PDB entries of the same protein (UniProt Q13153 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FXZ 1.64 Å, Crystal structure of PAK1 kinase domain with ruthenium complex lambda-FL172
2QME 1.75 Å, Crystal structure of human RAC3 in complex with CRIB domain of human p21-activated…
9N4U 1.77 Å, Crystal structure of PAK1 bound to compound R1
1YHV 1.8 Å, Crystal Structure of PAK1 kinase domain with two point mutations (K299R, T423E)
1YHW 1.8 Å, Crystal Structure of PAK1 kinase domain with one point mutations (K299R)
8X5Z 1.8 Å, The Crystal Structure of PAK1 kinase domain from Biortus.
3Q52 1.8 Å, Structure of phosphorylated PAK1 kinase domain
9D4V 1.84 Å, Structure of PAK1 in complex with compound 7
9D4X 1.85 Å, Structure of PAK1 in complex with compound 16
9D4Y 1.85 Å, Structure of PAK1 in complex with compound 31
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1
3Q4Z 1.89 Å, Structure of unphosphorylated PAK1 kinase domain

Browse structure collections

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