9QFF | pdb_00009qff

Structure of SOS1 in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.304 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.278 (Depositor) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Focused Structure-Based Virtual Screening Identifies Novel Inhibitors of SOS1.

Bonomo, S.Gibault, F.Bagal, S.K.Blackwell, J.H.Breed, J.Collie, G.W.Couturier, M.Diene, C.Di Fruscia, P.Gray, S.Hughes, C.Jeyaharan, D.Kettle, J.G.Milbradt, A.G.Northall, S.Peters, K.Stubbs, C.J.Underwood, E.Chen, Y.Hao, H.Lainchbury, M.D.

(2025) ACS Med Chem Lett 16: 1905-1909

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00302
  • Primary Citation Related Structures: 
    9QFF

  • PubMed Abstract: 

    SOS1 is one of the key regulators of KRAS where it catalyzes the GTP-to-GDP turnover required for KRAS activation. Inhibition of the SOS1::KRAS interaction is an attractive strategy to modulate abnormal KRAS activation, which is responsible for several malignancies. In this work, we performed a virtual screening campaign on the AstraZeneca compound collection with Heavy Atom Count between 21 and 26 and identified two novel and efficient binders of SOS1 which fulfill the minimal pharmacophoric requirements disclosed in known compounds. Subsequently, structure- and knowledge-based approaches were applied to develop these binders into functional inhibitors of SOS1.


  • Organizational Affiliation
    • Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.

Macromolecule Content 

  • Total Structure Weight: 57.72 kDa 
  • Atom Count: 3,585 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1490Homo sapiensMutation(s): 4 
Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
PHAROS:  Q07889
GTEx:  ENSG00000115904 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07889
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I6H
(Subject of Investigation/LOI)

Query on A1I6H



Download:Ideal Coordinates CCD File
B [auth A]3-[[3-(trifluoromethyl)phenyl]methyl]-2~{H}-1$l^{6},2,4-benzothiadiazine 1,1-dioxide
C15 H11 F3 N2 O2 S
IXHISIYNGIIOEL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.304 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.278 (Depositor) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.458α = 90
b = 84.691β = 90
c = 176.383γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-09-17 
  • Deposition Author(s): Breed, J.

Funding OrganizationLocationGrant Number
Other privateUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references