9E8M | pdb_00009e8m

Covalent inhibitor VVD-442 bound to the RAS binding domain (RBD) of PI3Ka


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.202 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9E8M

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Covalent inhibitors of the PI3K alpha RAS binding domain impair tumor growth driven by RAS and HER2.

Klebba, J.E.Roy, N.Bernard, S.M.Grabow, S.Hoffman, M.A.Miao, H.Tamiya, J.Wang, J.Berry, C.Esparza-Oros, A.Lin, R.Liu, Y.Pariollaud, M.Parker, H.Mochalkin, I.Rana, S.Snead, A.N.Walton, E.J.Wyrick, T.E.Aitichson, E.Bedke, K.Brannon, J.C.Chick, J.M.Hee, K.Horning, B.D.Ismail, M.Lamb, K.N.Lin, W.Lu, J.Pastuszka, M.K.Pollock, J.Sigler, J.J.Tomaschko, M.Tran, E.Yue, C.Kinsella, T.M.Molina-Arcas, M.Cook, B.N.Simon, G.M.Weinstein, D.S.Downward, J.Patricelli, M.P.

(2025) Science 390: 702-709

  • DOI: https://doi.org/10.1126/science.adv2684
  • Primary Citation Related Structures: 
    9E8M

  • PubMed Abstract: 

    Genetic disruption of the RAS binding domain (RBD) of phosphoinositide 3-kinase alpha (PI3Kα) impairs the growth of tumors driven by the small guanosine triphosphatase RAS in mice and does not affect PI3Kα's role in insulin-mediated control of glucose homeostasis. Selectively blocking the RAS-PI3Kα interaction may represent a strategy for treating RAS-dependent cancers as it avoids the toxicity associated with inhibitors of PI3Kα lipid kinase activity. We developed compounds that bind covalently to cysteine 242 in the RBD of PI3K p110α and block RAS activation of PI3Kα activity. In mice, inhibitors slow the growth of RAS mutant tumors and human epidermal growth factor receptor 2-overexpressing tumors, particularly when combined with other inhibitors of the RAS/mitogen-activated protein kinase pathway, without causing hyperglycemia.


  • Organizational Affiliation
    • Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 34.82 kDa 
  • Atom Count: 2,383 
  • Modeled Residue Count: 275 
  • 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
A1BF9
(Subject of Investigation/LOI)

Query on A1BF9



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
1-[(1P)-5-bromo-2'-chloro[1,1'-biphenyl]-2-sulfonyl]-4-fluoro-N-[(2S)-4-(methanesulfonyl)butan-2-yl]piperidine-4-carboxamide
C23 H27 Br Cl F N2 O5 S2
RBHNKTBCOAXEQK-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.202 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.39α = 90
b = 88.303β = 90
c = 139γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references
  • Version 1.2: 2025-11-19
    Changes: Database references
  • Version 1.3: 2025-11-26
    Changes: Database references