9D51: PAK2

Structure of PAK2 in complex with compound 12. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,576
Mol. weight: 67.26 kDa
Ligands: A1A2Q
Released: 2 Apr 2025

Explore 9D51 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D51 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	231-237	7
β-strand	241	1	3
α-helix	245-248	4
β-strand	249-256	8	3
β-strand	262-268	7	3
β-strand	273-281	9	3
α-helix	289-300	12
β-strand	306	1	4
α-helix	307-308	2
β-strand	309-315	7	3
β-strand	318-323	6	3
β-strand	329-330	2	4
α-helix	331-337	7
α-helix	342-361	20
β-strand	364-365	2	5
α-helix	371-373	3
β-strand	374-376	3	4
β-strand	382-384	3	4
β-strand	391-392	2	5
α-helix	407-409	3
α-helix	412-415	4
α-helix	424-438	15
α-helix	448-458	11
α-helix	461-463	3
α-helix	466-468	3
α-helix	471-480	10
α-helix	489-490	2
α-helix	491-494	4
α-helix	498-500	3
α-helix	503-505	3
α-helix	506-509	4
α-helix	510-520	11

Chain B: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	240	1	1
α-helix	241	1
α-helix	245-248	4
β-strand	249-256	8	1
β-strand	262-268	7	1
β-strand	274-281	8	1
α-helix	292-294	3
α-helix	295-300	6
β-strand	306	1	2
β-strand	309-315	7	1
β-strand	318-324	7	1
β-strand	328-330	3	2
α-helix	331-337	7
α-helix	342-361	20
α-helix	371-373	3
β-strand	374-377	4	2
β-strand	382-384	3	2
α-helix	402-403	2
α-helix	412-415	4
α-helix	423-438	16
α-helix	448-457	10
α-helix	466-468	3
α-helix	471-480	10
α-helix	489-490	2
α-helix	491-494	4
α-helix	498-502	5
α-helix	503-505	3
α-helix	506-509	4
α-helix	510-519	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PAK-2p34	A, B	protein	297	Homo sapiens	Q13177 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9D51_1 PAK-2p34 (chains A, B)
TDEEIMEKLRTIVSIGDPKKKYTRYEKIGQGASGTVFTATDVALGQEVAIKQINLQKQPK
KELIINEILVMKELKNPNIVNFLDSYLVGDELFVVMEYLAGGSLTDVVTETCMDEAQIAA
VCRECLQALEFLHANQVIHRNIKSDNVLLGMEGSVKLTDFGFCAQITPEQSKRSEMVGTP
YWMAPEVVTRKAYGPKVDIWSLGIMAIEMVEGEPPYLNENPLRALYLIATNGTPELQNPE
KLSPIFRDFLNRCLEMDVEKRGSAKELLQHQFLKLAKPLSSLTPLIAAAKEAMKSNR

Ligands and cofactors

ID	Name	Formula	Copies
A1A2Q	N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-[5-(trifluoromethyl)-1,3-thiazol-…	C15 H19 F3 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 Q13177 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WS3 1.85 Å, Crystal structure of phosphorylated PAK2 kinase domain containing K278R mutant
9WS2 1.9 Å, Crystal structure of nucleotide-bound PAK2 kinase domain containing K278R mutant
9WS6 2.0 Å, Crystal structure of AMP-PNP-bound PAK2 kinase domain containing D368N mutant
9WS5 2.4 Å, Crystal structure of PAK2 kinase domain containing D368N mutant
9LBF 2.62 Å, The crystal structure of the truncated PAK2 containing D368N mutant
3PCS 2.86 Å, Structure of EspG-PAK2 autoinhibitory Ialpha3 helix complex
9LBG 2.89 Å, The crystal structure of the truncated PAK2 containing K278R mutant
9M41 3.02 Å, The crystal structure of full-length PAK2 containing K278R and D368N mutants

Browse structure collections

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