9BVF | pdb_00009bvf

Identification of multiple ligand hotspots on SOS2, compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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Literature

Discovery of Small Molecules that Bind to Son of Sevenless 2 (SOS2).

Zak, K.M.Waterson, A.G.Geist, L.Braun, N.Hauer, K.Rumpel, K.Ramharter, J.Stadtmueller, H.Wolkerstorfer, B.Schoenbauer, D.Cui, J.Phan, J.Abbott, J.R.Sarkar, D.Hodges, T.R.Arnold, A.Sensintaffar, J.L.Fesik, S.W.Kessler, D.

(2025) J Med Chem 68: 2680-2693

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02007
  • Primary Citation of Related Structures:  
    9BVE, 9BVF, 9BVI, 9GIN

  • PubMed Abstract: 

    The Son of Sevenless (SOS) protein family includes two highly homologous proteins, SOS1 and SOS2, that act as guanine nucleotide exchange factors (GEFs) for RAS proteins. They catalyze the GDP-to-GTP exchange, resulting in an increase of the active GTP-bound form of RAS. Despite highly similar structures and expression patterns, SOS1 is generally accepted as the dominant RAS GEF for downstream signaling in pathological states. Nonetheless, SOS2 has been reported to critically impact the RAS-PI3K/AKT signaling axis, especially in KRAS-driven cancer cell lines and in the absence of SOS1. Hence, therapeutic targeting of SOS2 may be an attractive strategy to target RAS-driven malignancies. Herein, we report the discovery and initial optimization of a selective quinazoline-based compound series that binds with micromolar affinity to the catalytic site of SOS2. We also disclose an additional, previously unreported binding site on SOS2 occupied by a different small molecule class.


  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG, A-1121 Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Son of sevenless homolog 2514Homo sapiensMutation(s): 0 
Gene Names: SOS2
UniProt & NIH Common Fund Data Resources
Find proteins for Q07890 (Homo sapiens)
Explore Q07890 
Go to UniProtKB:  Q07890
PHAROS:  Q07890
GTEx:  ENSG00000100485 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07890
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.016α = 90
b = 86.246β = 90
c = 107.238γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1ASXClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Lustgarten FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references