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⇱ RCSB PDB - 4JPS: Co-crystal Structures of the Lipid Kinase PI3K alpha with Pan and Isoform Selective Inhibitors

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251,806
Structures from the PDB archive		1,068,577
Computed Structure Models (CSM)

 4JPS | pdb_00004jps

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

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) 

wwPDB Validation  3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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 Search on PubMed
  • DOI: https://doi.org/10.1016/j.bmcl.2013.05.007
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Novartis Institutes for BioMedical Research, WKL-136.4.12, CH-4002 Basel, Switzerland.

Macromolecule Content 

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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform1,074Homo sapiensMutation(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)
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UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
PHAROS:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha293Homo sapiensMutation(s): 0 
Gene Names: GRB1, PIK3R1
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UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1LT
Query on 1LT
Download Ideal Coordinates CCD File 
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		👁 Image
SCN
Query on SCN
Download Ideal Coordinates CCD File 
C [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		👁 Image
Binding Affinity Annotations 
IDSourceBinding Affinity
1LT BindingDB:  4JPS IC50: min: 1.7, max: 1837 (nM) from 15 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 = 104.865α = 90
b = 106.195β = 90
c = 133.667γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.