4JPS | pdb_00004jps

Co-crystal Structures of the Lipid Kinase PI3K alpha with Pan and Isoform Selective Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4JPS/pdb

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


• Deposited: 2013-03-19 Released: 2014-04-02 
• Deposition Author(s): Knapp, M.S., Elling, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Discovery of NVP-BYL719 a potent and selective phosphatidylinositol-3 kinase alpha inhibitor selected for clinical evaluation.

Furet, P., Guagnano, V., Fairhurst, R.A., Imbach-Weese, P., Bruce, I., Knapp, M., Fritsch, C., Blasco, F., Blanz, J., Aichholz, R., Hamon, J., Fabbro, D., Caravatti, G.

(2013) Bioorg Med Chem Lett 23: 3741-3748

• PubMed: 23726034 
• DOI: https://doi.org/10.1016/j.bmcl.2013.05.007
• Primary Citation of Related Structures:  
  4JPS


• PubMed Abstract: 
  

  Phosphatidylinositol-3-kinase α (PI3Kα) is a therapeutic target of high interest in anticancer drug research. On the basis of a binding model rationalizing the high selectivity and potency of a particular series of 2-aminothiazole compounds in inhibiting PI3Kα, a medicinal chemistry program has led to the discovery of the clinical candidate NVP-BYL719.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, WKL-136.4.12, CH-4002 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 160.93 kDa 
• Atom Count: 10,533 
• Modelled Residue Count: 1,226 
• Deposited Residue Count: 1,367 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	1,074	Homo sapiens	Mutation(s): 2  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	293	Homo sapiens	Mutation(s): 0  Gene Names: GRB1, PIK3R1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens) Explore P27986  Go to UniProtKB:  P27986
PHAROS:  P27986 GTEx:  ENSG00000145675

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1LT	D [auth A]	(2S)-N~1~-{4-methyl-5-[2-(1,1,1-trifluoro-2-methylpropan-2-yl)pyridin-4-yl]-1,3-thiazol-2-yl}pyrrolidine-1,2-dicarboxamide C19 H22 F3 N5 O2 S STUWGJZDJHPWGZ-LBPRGKRZSA-N
SCN	C [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
1LT	BindingDB:  4JPS	IC50: min: 3, max: 1837 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.865	α = 90
b = 106.195	β = 90
c = 133.667	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XSCALE	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Knapp, M.S., Elling, R.A.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-10-12
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-05-22
  Changes: Data collection