5KBQ

Pak1 in complex with bis-anilino pyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5KBQ/pdb

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


• Deposited: 2016-06-03 Released: 2016-09-28 
• Deposition Author(s): Ferguson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.230 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Optimization of Highly Kinase Selective Bis-anilino Pyrimidine PAK1 Inhibitors.

McCoull, W., Hennessy, E.J., Blades, K., Chuaqui, C., Dowling, J.E., Ferguson, A.D., Goldberg, F.W., Howe, N., Jones, C.R., Kemmitt, P.D., Lamont, G., Varnes, J.G., Ward, R.A., Yang, B.

(2016) ACS Med Chem Lett 7: 1118-1123

• PubMed: 27994749 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00322
• Primary Citation of Related Structures:  
  5KBQ, 5KBR


• PubMed Abstract: 
  

  Group I p21-activated kinase (PAK) inhibitors are indicated as important in cancer progression, but achieving high kinase selectivity has been challenging. A bis-anilino pyrimidine PAK1 inhibitor was identified and optimized through structure-based drug design to improve PAK1 potency and achieve high kinase selectivity, giving in vitro probe compound AZ13705339 ( 18 ). Reduction of lipophilicity to lower clearance afforded AZ13711265 ( 14 ) as an in vivo probe compound with oral exposure in mouse. Such probes will allow further investigation of PAK1 biology.

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Organizational Affiliation: 

AstraZeneca , 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, U.K.

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.

Macromolecule Content

• Total Structure Weight: 65.15 kDa 
• Atom Count: 4,483 
• Modelled Residue Count: 562 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 1	A, B	289	Homo sapiens	Mutation(s): 3  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
GTEx:  ENSG00000149269

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPV	C [auth A]	[4-methyl-3-[methyl-[2-[(3-methylsulfonyl-5-morpholin-4-yl-phenyl)amino]pyrimidin-4-yl]amino]phenyl]methanol C24 H29 N5 O4 S IVWHSTCJCURGMH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IPV	BindingDB:  5KBQ	IC50: min: 100, max: 3100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.230 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.911	α = 90
b = 80.94	β = 107.07
c = 66.022	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Ferguson, A.

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2017-01-11
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description