4ZOP | pdb_00004zop

Co-crystal Structure of Lipid Kinase PI3K alpha with a selective phosphatidylinositol-3 kinase alpha inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZOP/pdb

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


• Deposited: 2015-05-06 Released: 2016-05-18 
• Deposition Author(s): Knapp, M.S., Elling, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Co-crystal Structure of the Lipid Kinase PI3K alpha with a selective phosphatidylinositol-3 kinase alpha inhibitorCo-crystal Structure of the Lipid Kinase PI3K alpha with a selective phosphatidylinositol-3 kinase alpha inhibitor

Fairhurst, R.A., Gerspacher, M., Imbach-Weese, P., Mah, R., Caravatti, G., Fuert, P., Fritsch, C., Schnell, C., Blanz, J., Blasco, F., Desrayaud, S., Guthy, D.A., Knapp, M.S., Arz, D., Wirth, J., Roehn-Carnemolla, E., Luu, V.H.

To be published.

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: 160.46 kDa 
• Atom Count: 10,201 
• Modelled Residue Count: 1,240 
• Deposited Residue Count: 1,364 
• 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	290	Homo sapiens	Mutation(s): 0  Gene Names: PIK3R1, GRB1
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4Q2	C [auth A]	(2S,3R)-N~1~-(8-tert-butyl-4,5-dihydro[1,3]thiazolo[4,5-h]quinazolin-2-yl)-3-methylpyrrolidine-1,2-dicarboxamide C20 H26 N6 O2 S NUGMMEMSYIUTGA-YGRLFVJLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4Q2	BindingDB:  4ZOP	IC50: min: 4, max: 6 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.812	α = 90
b = 106.558	β = 90
c = 134.788	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Knapp, M.S., Elling, R.A.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description