4PS3

Structure of PI3K gamma in complex with 1-[6-(5-methoxypyridin-3-yl)-1,3-benzothiazol-2-yl]-3-[2-(1-propyl-1H-imidazol-4-yl)ethyl]urea

• PDB DOI: https://doi.org/10.2210/pdb4PS3/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-03-06 Released: 2014-05-14 
• Deposition Author(s): Griffith, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Structural Basis for Isoform Selectivity in a Class of Benzothiazole Inhibitors of Phosphoinositide 3-Kinase gamma.

Collier, P.N., Martinez-Botella, G., Cornebise, M., Cottrell, K.M., Doran, J.D., Griffith, J.P., Mahajan, S., Maltais, F., Moody, C.S., Huck, E.P., Wang, T., Aronov, A.M.

(2015) J Med Chem 58: 517-521

• PubMed: 24754609 
• DOI: https://doi.org/10.1021/jm500362j
• Primary Citation of Related Structures:  
  4PS3, 4PS7, 4PS8


• PubMed Abstract: 
  

  Phosphoinositide 3-kinase γ (PI3Kγ) is an attractive target to potentially treat a range of disease states. Herein, we describe the evolution of a reported phenylthiazole pan-PI3K inhibitor into a family of potent and selective benzothiazole inhibitors. Using X-ray crystallography, we discovered that compound 22 occupies a previously unreported hydrophobic binding cleft adjacent to the ATP binding site of PI3Kγ, and achieves its selectivity by exploiting natural sequence differences among PI3K isoforms in this region.

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Organizational Affiliation: 

Vertex Pharmaceuticals Inc. , 50 Northern Avenue, Boston, Massachusetts 02210, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 111.19 kDa 
• Atom Count: 6,881 
• Modelled Residue Count: 843 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 0  Gene Names: PI3K gamma, PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2WH	B [auth A]	1-[6-(5-methoxypyridin-3-yl)-1,3-benzothiazol-2-yl]-3-[2-(1-propyl-1H-imidazol-4-yl)ethyl]urea C22 H24 N6 O2 S VYPWROGLWNYKDD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2WH	BindingDB:  4PS3	Ki: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.689	α = 90
b = 67.788	β = 96.16
c = 106.12	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Griffith, J.P.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2015-01-21
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations