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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.228 (Depositor), 0.234 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (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

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42336
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1LT Query on 1LT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding 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), 0.234 (DCC)
R-Value Work: 0.205 (Depositor), 0.208 (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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Knapp, M.S.

Elling, R.A.

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