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 ?
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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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Identification of a p21-Activated Kinase 1 (PAK1) Inhibitor with 10-fold Selectivity Against PAK2

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

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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 ?
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 ( ? )	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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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

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.