4O0T

Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb4O0T/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-14 Released: 2014-02-12 
• Deposition Author(s): Oh, A., Tam, C., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 

Literature

Back Pocket Flexibility Provides Group II p21-Activated Kinase (PAK) Selectivity for Type I 1/2 Kinase Inhibitors.

Staben, S.T., Feng, J.A., Lyle, K., Belvin, M., Boggs, J., Burch, J.D., Chua, C.C., Cui, H., Dipasquale, A.G., Friedman, L.S., Heise, C., Koeppen, H., Kotey, A., Mintzer, R., Oh, A., Roberts, D.A., Rouge, L., Rudolph, J., Tam, C., Wang, W., Xiao, Y., Young, A., Zhang, Y., Hoeflich, K.P.

(2014) J Med Chem 57: 1033-1045

• PubMed: 24432870 
• DOI: https://doi.org/10.1021/jm401768t
• Primary Citation of Related Structures:  
  4O0R, 4O0T, 4O0V, 4O0X, 4O0Y


• PubMed Abstract: 
  

Structure-based methods were used to design a potent and highly selective group II p21-activated kinase (PAK) inhibitor with a novel binding mode, compound 17. Hydrophobic interactions within a lipophilic pocket past the methionine gatekeeper of group II PAKs approached by these type I 1/2 binders were found to be important for improving potency. A structure-based hypothesis and strategy for achieving selectivity over group I PAKs, and the broad kinome, based on unique flexibility of this lipophilic pocket, is presented. A concentration-dependent decrease in tumor cell migration and invasion in two triple-negative breast cancer cell lines was observed with compound 17.

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Organizational Affiliation: 

Department of Discovery Chemistry, ‡Department of Translational Oncology, △Department of Pathology, §Department of Drug Metabolism and Pharmacokinetics, ∥Department of Biochemical and Cellular Pharmacology, and ⊥Department of Structural Biology, Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.5 kDa 
• Atom Count: 4,489 
• Modelled Residue Count: 572 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 1	A, B	300	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2OL	C [auth A]	1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol C22 H26 N6 O2 RZXMIHOUHYSGJO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2OL	BindingDB:  4O0T	Ki: 2900 (nM) from 1 assay(s)
		IC50: min: 970, max: 1.00e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.214 
• R-Value Observed: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.656	α = 90
b = 79.17	β = 106.97
c = 66.343	γ = 90

Software Package:

Software Name	Purpose
B3	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Oh, A., Tam, C., Wang, W.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references