7UKS | pdb_00007uks

Crystal structure of SOS1 with phthalazine inhibitor bound (compound 15)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.275 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

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 NL0Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Design and Discovery of MRTX0902, a Potent, Selective, Brain-Penetrant, and Orally Bioavailable Inhibitor of the SOS1:KRAS Protein-Protein Interaction.

Ketcham, J.M.Haling, J.Khare, S.Bowcut, V.Briere, D.M.Burns, A.C.Gunn, R.J.Ivetac, A.Kuehler, J.Kulyk, S.Laguer, J.Lawson, J.D.Moya, K.Nguyen, N.Rahbaek, L.Saechao, B.Smith, C.R.Sudhakar, N.Thomas, N.C.Vegar, L.Vanderpool, D.Wang, X.Yan, L.Olson, P.Christensen, J.G.Marx, M.A.

(2022) J Med Chem 65: 9678-9690

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00741
  • Primary Citation of Related Structures:  
    7UKR, 7UKS

  • PubMed Abstract: 

    SOS1 is one of the major guanine nucleotide exchange factors that regulates the ability of KRAS to cycle through its "on" and "off" states. Disrupting the SOS1:KRAS G12C protein-protein interaction (PPI) can increase the proportion of GDP-loaded KRAS G12C , providing a strong mechanistic rationale for combining inhibitors of the SOS1:KRAS complex with inhibitors like MRTX849 that target GDP-loaded KRAS G12C . In this report, we detail the design and discovery of MRTX0902─a potent, selective, brain-penetrant, and orally bioavailable SOS1 binder that disrupts the SOS1:KRAS G12C PPI. Oral administration of MRTX0902 in combination with MRTX849 results in a significant increase in antitumor activity relative to that of either single agent, including tumor regressions in a subset of animals in the MIA PaCa-2 tumor mouse xenograft model.


  • Organizational Affiliation

    Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1487Homo sapiensMutation(s): 0 
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
NL0 (Subject of Investigation/LOI)
Query on NL0

Download Ideal Coordinates CCD File 
B [auth A]4-methyl-N-{(1R)-1-[2-methyl-3-(trifluoromethyl)phenyl]ethyl}-7-(piperazin-1-yl)phthalazin-1-amine
C23 H26 F3 N5
MJSKXOIIHARCLW-OAHLLOKOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NL0 BindingDB:  7UKS Ki: min: 0.11, max: 0.33 (nM) from 2 assay(s)
IC50: 47 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.792α = 90
b = 89.102β = 90
c = 172.316γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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 NL0Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Structure summary
  • Version 1.2: 2022-08-10
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description