9D4Y | pdb_00009d4y

Structure of PAK1 in complex with compound 31

PDB DOI: https://doi.org/10.2210/pdb9D4Y/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-08-13 Released: 2025-04-02
Deposition Author(s): Fontano, E., Suto, R.K., Olland, A.M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.227 (Depositor), 0.228 (DCC)
R-Value Work:
0.188 (Depositor), 0.196 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

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.

(2025) Bioorg Med Chem Lett 127: 130307-130307

PubMed: 40516764 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2025.130307
Primary Citation Related Structures:
9D4V, 9D4W, 9D4X, 9D4Y, 9D50, 9D51, 9D52, 9D53

PubMed Abstract:
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.

Organizational Affiliation

Turning Point Therapeutics, Inc. (a wholly owned subsidiary of Bristol Myers Squibb Company), 10628 Science Center Drive, Suite 200, San Diego, CA 92121, United States. Electronic address: deidre123@gmail.com.

Macromolecule Content

Total Structure Weight: 67.48 kDa
Atom Count: 4,582
Modeled Residue Count: 571
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 1	A, B	297	Homo sapiens	Mutation(s): 2 Gene Names: PAK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens) Explore Q13153 Go to UniProtKB: Q13153
PHAROS: Q13153 GTEx: ENSG00000149269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A2S (Subject of Investigation/LOI) Query on A1A2S Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N~2~-{[(1R,3R,4S)-4-amino-3-(3-chlorophenyl)cyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine C₂₃ H₂₇ Cl N₆ S RPZYQSABIKMHOM-ZMYBRWDISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.227 (Depositor), 0.228 (DCC)
R-Value Work: 0.188 (Depositor), 0.196 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.306	α = 90
b = 80.946	β = 106.61
c = 65.883	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release
Version 1.1: 2025-06-25
Changes: Database references
Version 1.2: 2025-07-16
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.