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


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1BF9Click on this verticalbar to view details

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Literature

Covalent inhibitors of the RAS binding domain of PI3K alpha 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.Metzger, J.Pastuszka, M.K.Pollock, J.Sigler, J.J.Tomaschko, M.Tran, E.Kinsella, T.M.Molina-Arcas, M.Simon, G.M.Weinstein, D.S.Downward, J.Patricelli, M.P.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.12.17.629001
  • Primary Citation of Related Structures:  
    9E8M

  • PubMed Abstract: 

    Genetic disruption of the RAS binding domain (RBD) of PI 3-kinase (PI3K) prevents the growth of mutant RAS driven tumors in mice and does not impact PI3K's role in insulin mediated control of glucose homeostasis. Selectively blocking the RAS-PI3K interaction may represent an attractive strategy for treating RAS-dependent cancers as it would avoid the toxicity associated with inhibitors of PI3K lipid kinase activity such as alpelisib. Here we report compounds that bind covalently to cysteine 242 in the RBD of PI3K p110α and block the ability of RAS to activate PI3K activity. These inhibitors have a profound impact on the growth of RAS mutant and also HER2 over-expressing tumors, particularly when combined with other inhibitors of the RAS/MAPK pathway, without causing hyperglycemia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1BF9Click on this verticalbar to view details

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