ISDA

Deposition Date 2024-08-13

Release Date 2025-04-02

Last Version Date 2025-07-16

Entry Detail

PDB ID:

9D4X

Keywords:

TRANSFERASE

Title:

Structure of PAK1 in complex with compound 16

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.85 Å

R-Value Free:

0.22

R-Value Work:

0.18

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Serine/threonine-protein kinase PAK 1
Gene (Uniprot):PAK1
Mutations:D389N, T423E
Chain IDs:A, B
Chain Length:296
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q13153 Pfam ID:PF00069 EC:2.7.11.1

Ligand Molecules

A1A2S

Primary Citation

Identification of a p21-activated kinase 1 (PAK1) inhibitor with 10-fold selectivity against PAK2.

Johns, D.M, Olejniczak, J, Babbar, A, Boone, C.D, Cakici, O, Cheng, M, Cheng, Q.Q, Dementiev, A, Eick, M, Ferdyan, N, Fontano, E, Forman, A, Kozlowski, R, Lee, S.W, Mehta, S, Mowery, K, Murray, B, Nguyen, V, Olland, A, Phan, K.B, Rivera, L, Sabat, M, Sprengeler, P, Srinivasan, K, Sun, Z, Suto, R.K, Wilkinson, T, Wang, C, Yu, N, Xu, M, Goel, V, Hirst, G, Reich, S.Show

Bioorg.Med.Chem.Lett. 127 130307 130307 (2025)

PMID: 40516764 DOI: 10.1016/j.bmcl.2025.130307

Abstact

The p21-activated kinases (PAKs) are noted for their role in cytoskeletal organization, cellular morphogenesis, and pro-survival signaling. PAK1 is of particular interest due to its role in tumorigenesis, being amplified in multiple cancers (the most prevalent being breast, ovarian, and melanoma cancers). PAK2 is closely related to PAK1 in structure but is associated with cardiotoxicity. A structure-based design effort targeting a PAK1 (over PAK2) selective small molecule inhibitor is detailed herein. We report here the first crystal structure of PAK2 and use this crystal structure to design a PAK1 inhibitor with ten-fold selectivity over PAK2.

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Primary Citation of related structures