9D4Y: PAK1

Structure of PAK1 in complex with compound 31. Determined by X-ray diffraction at 1.85 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,582
Mol. weight: 67.48 kDa
Ligands: A1A2S
Released: 2 Apr 2025

Explore 9D4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D4Y contains 38 α-helices and 23 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	254-260	7
β-strand	262	1	1
α-helix	266-269	4
β-strand	270-277	8	1
β-strand	283-289	7	1
β-strand	295-302	8	1
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	349-351	3	2
α-helix	352-358	7
α-helix	363-382	20
β-strand	385-386	2	3
α-helix	392-394	3
β-strand	395-398	4	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	445-459	15
α-helix	469-479	11
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: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	257-260	4
α-helix	266-269	4
β-strand	270-275	6	5
β-strand	283-289	7	5
β-strand	295-302	8	5
α-helix	309-321	13
β-strand	327	1	6
β-strand	330-336	7	5
β-strand	339-345	7	5
β-strand	349-351	3	6
α-helix	352-358	7
α-helix	363-382	20
α-helix	392-394	3
β-strand	395-398	4	6
β-strand	402-405	4	6
α-helix	422-424	3
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	531-542	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PAK 1	A, B	protein	297	Homo sapiens	Q13153 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9D4Y_1 Serine/threonine-protein kinase PAK 1 (chains A, B)
SDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPK
KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAA
VCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTP
YWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPE
KLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNH

Ligands and cofactors

ID	Name	Formula	Copies
A1A2S	N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopro…	C23 H27 Cl N6 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
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1
3Q4Z 1.89 Å, Structure of unphosphorylated PAK1 kinase domain
9D50 1.9 Å, Structure of PAK1 in complex with compound 24

Browse structure collections

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