5DEW

Crystal structure of PAK1 in complex with an inhibitor compound 5

• PDB DOI: https://doi.org/10.2210/pdb5DEW/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-08-26 Released: 2016-09-21 
• Deposition Author(s): Oh, A., Tam, C., Wang, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Design of Selective PAK1 Inhibitor G-5555: Improving Proper-ties by Employing an Unorthodox Low-pKa Polar Moiety

Ndubaku, C.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.58 kDa 
• Atom Count: 5,019 
• Modelled Residue Count: 576 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
59N	C [auth A], D [auth B]	8-[(trans-4-aminocyclohexyl)methyl]-6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]-2-(ethylamino)pyrido[2,3-d]pyrimidin-7(8H)-one C27 H30 Cl N7 O PJYRMGKJLXENCU-IRJFHVNHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
59N	BindingDB:  5DEW	Ki: 1.9 (nM) from 1 assay(s)
		IC50: 124 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.215 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.556	α = 90
b = 81.053	β = 106.39
c = 66.499	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Oh, A., Tam, C., Wang, W.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations