6GVG | pdb_00006gvg

Crystal structure of PI3K alpha in complex with 3-(2-Amino-benzooxazol-5-yl)-1-isopropyl-4-methyl-1H-pyrazolo[3,4-d]pyrimidin-6-ylamine

• PDB DOI: https://doi.org/10.2210/pdb6GVG/pdb

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


• Deposited: 2018-06-21 Released: 2019-10-02 
• Deposition Author(s): Ouvry, G., Aurelly, M., Bonnary, L., Borde, E., Bouix-Peter, C., Chantalat, L., Clary, L., Defoin-Platel, C., Deret, S., Forissier, M., Harris, C.S., Isabet, T., Lamy, L., Luzy, A.P., Pascau, J., Soulet, C., Taddei, A., Taquet, N., Tomas, L., Thoreau, E., Varvier, E., Vial, E., Hennequin, L.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Impact of Minor Structural Modifications on Properties of a Series of mTOR Inhibitors.

Ouvry, G., Clary, L., Tomas, L., Aurelly, M., Bonnary, L., Borde, E., Bouix-Peter, C., Chantalat, L., Defoin-Platel, C., Deret, S., Forissier, M., Harris, C.S., Isabet, T., Lamy, L., Luzy, A.P., Pascau, J., Soulet, C., Taddei, A., Taquet, N., Thoreau, E., Varvier, E., Vial, E., Hennequin, L.F.

(2019) ACS Med Chem Lett 10: 1561-1567

• PubMed: 31749911 
• DOI: https://doi.org/10.1021/acsmedchemlett.9b00401
• Primary Citation of Related Structures:  
  6GVF, 6GVG, 6GVH, 6GVI


• PubMed Abstract: 
  

  Minor structural modifications-sometimes single atom changes-can have a dramatic impact on the properties of compounds. This is illustrated here on structures related to known mTOR inhibitor Sapanisertib. Subtle changes in the hinge binder lead to strikingly different overall profiles with changes in physical properties, metabolism, and kinase selectivity.

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Organizational Affiliation: 

Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France.

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: 112.38 kDa 
• Atom Count: 7,424 
• Modeled Residue Count: 910 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	962	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FCZ	B [auth A]	5-(6-azanyl-4-methyl-1-propan-2-yl-pyrazolo[3,4-d]pyrimidin-3-yl)-1,3-benzoxazol-2-amine C16 H17 N7 O LGAJJTHJWVAHRF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FCZ	BindingDB:  6GVG	Ki: 990 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.229 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.45	α = 90
b = 135.86	β = 90
c = 142.58	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
MxCuBE	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Ouvry, G., Aurelly, M., Bonnary, L., Borde, E., Bouix-Peter, C., Chantalat, L., Clary, L., Defoin-Platel, C., Deret, S., Forissier, M., Harris, C.S., Isabet, T., Lamy, L., Luzy, A.P., Pascau, J., Soulet, C., Taddei, A., Taquet, N., Tomas, L., Thoreau, E., Varvier, E., Vial, E., Hennequin, L.F.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Advisory, Data collection, Database references