9B4U | pdb_00009b4u

Crystal structure of p110alpha-RBD covalently bound to a breaker compound BBO-10203 via Cys242


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.269 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

BBO-10203 inhibits tumor growth without inducing hyperglycemia by blocking RAS-PI3K alpha interaction.

Simanshu, D.K.Xu, R.Stice, J.P.Czyzyk, D.J.Feng, S.Denson, J.P.Riegler, E.Yang, Y.Zhang, C.Donovan, S.Smith, B.P.Abreu-Blanco, M.Chen, M.Feng, C.Fu, L.Rabara, D.Young, L.C.Dyba, M.Yan, W.Lin, K.Ghorbanpoorvalukolaie, S.Larsen, E.K.Malik, W.Champagne, A.Parker, K.Ju, J.H.Jeknic, S.Esposito, D.Turner, D.M.Lightstone, F.C.Wang, B.Wehn, P.M.Wang, K.Stephen, A.G.Maciag, A.E.Hata, A.N.Sinkevicius, K.W.Nissley, D.V.Wallace, E.M.McCormick, F.Beltran, P.J.

(2025) Science 389: 409-415

  • DOI: https://doi.org/10.1126/science.adq2004
  • Primary Citation Related Structures: 
    9B4U

  • PubMed Abstract: 

    BBO-10203 is an orally available drug that covalently and specifically binds to the RAS-binding domain of phosphoinositide 3-kinase α (PI3Kα), preventing its activation by HRAS, NRAS, and KRAS. It inhibited PI3Kα activation in tumors with oncogenic mutations in KRAS or PIK3CA , and in tumors with human epidermal growth factor receptor 2 (HER2) amplification or overexpression. In preclinical models, BBO-10203 caused significant tumor growth inhibition across multiple tumor types and showed enhanced efficacy in combination with inhibitors of cyclin-dependent kinase 4/6 (CDK4/6), estrogen receptor (ER), HER2 and KRAS-G12C mutant, including in tumors harboring mutations in Kelch-like ECH-associated protein 1 (KEAP1) and Serine/Threonine Kinase 11 (STK11). Notably, these antitumor effects occurred without inducing hyperglycemia, as insulin signaling does not depend on RAS-mediated PI3Kα activation to promote glucose uptake.


  • Organizational Affiliation
    • NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 34.89 kDa 
  • Atom Count: 2,419 
  • Modeled Residue Count: 284 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
A, B
144Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AIR
(Subject of Investigation/LOI)

Query on A1AIR



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1-[(4R,8R)-2-[(4M,7P)-7-[2,4-difluoro-6-(2-methoxyethoxy)phenyl]-4-(1-methyl-1H-indazol-5-yl)thieno[3,2-c]pyridin-6-yl]-4-methyl-6,7-dihydropyrazolo[1,5-a]pyrazin-5(4H)-yl]propan-1-one
C34 H32 F2 N6 O3 S
HJERNIUFXRDZFD-LJQANCHMSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.269 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.041α = 90
b = 71.613β = 90
c = 62.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States75N91019D00024

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references