5XGJ | pdb_00005xgj

Crystal structure of PI3K complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5XGJ/pdb

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


• Deposited: 2017-04-13 Released: 2018-04-25 
• Deposition Author(s): Song, K., Yang, X., Zhao, Y., Jian, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of PI3K complex with an inhibitor

Song, K., Yang, X., Zhao, Y., Jian, Z.

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: 156.13 kDa 
• Atom Count: 10,430 
• Modeled Residue Count: 1,258 
• Deposited Residue Count: 1,326 
• 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	1,048	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase regulatory subunit alpha	B	278	Homo sapiens	Mutation(s): 0  Gene Names: 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
84X	C [auth A]	3-(4-morpholin-4-ylfuro[3,2-d]pyrimidin-2-yl)-5-[(phenylmethyl)amino]phenol C23 H22 N4 O3 NOLJEVWXVAGNIQ-UHFFFAOYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.877	α = 90
b = 136.368	β = 90
c = 149.028	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-25 
Deposition Author(s): Song, K., Yang, X., Zhao, Y., Jian, Z.

Revision History  

• Version 1.0: 2018-04-25
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references