9YF2 | pdb_00009yf2

Crystal structure of PI3Ka H1047R mutant in complex with PRT7140 in allosteric pocket

• PDB DOI: https://doi.org/10.2210/pdb9YF2/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): Yes 


• Deposited: 2025-09-25 Released: 2026-09-30 
• Deposition Author(s): Wang, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free: 
  0.295 (Depositor), 0.380 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.349 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Discovery of Tetrasubstituted Quinazolin-4(3 H )-ones as Wild-type-sparing, Highly Selective PI3K alpha H1047R Inhibitors

Chen, C., Holmes, R., Carter, J., Maity, S., Pawley, S., Stahl, N., Crossan, A., Rager, J., Juvekar, A., Wang, M., Xu, C., Kuskovsky, R., Sivakumar, M., Gallagher, K., Leal, R., Geeganage, S., Scherle, P., Combs, A., Buesking, A.

(2026) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.6c00269

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 156.93 kDa 
• Atom Count: 10,516 
• Modeled Residue Count: 1,268 
• Deposited Residue Count: 1,329 
• 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	1,068	Homo sapiens	Mutation(s): 1  Gene Names: PIK3CA EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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 [auth C]	261	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CV8( Subject of Investigation/LOI)	C [auth A]	2-({(1R)-1-[2-(1,3-dihydro-2H-isoindol-2-yl)-6-methyl-3-(oxan-4-yl)-4-oxo-3,4-dihydroquinazolin-8-yl]ethyl}amino)benzoic acid C31 H32 N4 O4 TYEGOGRZYHRNKH-HXUWFJFHSA-N
X3N (Subject of Investigation/LOI)	D [auth A]	N~2~-{(4S,11aP)-2-[(4S)-4-(difluoromethyl)-2-oxo-1,3-oxazolidin-3-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}-L-alaninamide C18 H19 F2 N5 O4 SGEUNORSOZVTOL-CABZTGNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free:  0.295 (Depositor), 0.380 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.349 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.99	α = 90
b = 125.78	β = 91.5
c = 167.45	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Wang, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release