9CML | pdb_00009cml

Crystal structure of p110alpha-RAS binding domain (RBD) in complex with molecular glue D223

• PDB DOI: https://doi.org/10.2210/pdb9CML/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-15 Released: 2025-07-23 
• Deposition Author(s): Czyzyk, D.J., Simanshu, D.K.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Molecular glues that facilitate RAS binding to PI3Kalpha promote glucose uptake without insulin

Czyzyk, D.J., Yan, W., Messing, S., Gillette, W., Esposito, D., Nissley, D.V., McCormick, F., Simanshu, D.K.

(2025) Science 

• DOI: https://doi.org/10.1126/science.adr9097

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.17 kDa 
• Atom Count: 2,430 
• Modeled Residue Count: 268 
• Deposited Residue Count: 282 
• 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, B	141	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AZD (Subject of Investigation/LOI)	C [auth A], D [auth B]	tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate C29 H32 F N5 O5 S NFCHONNVHGPRMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.041	α = 90
b = 91.173	β = 113.02
c = 47.944	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Czyzyk, D.J., Simanshu, D.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	75N91019D00024

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release