6SCM | pdb_00006scm

SOS1 in Complex with Inhibitor BI-3406


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.220 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6SCM

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

BI-3406, a Potent and Selective SOS1-KRAS Interaction Inhibitor, Is Effective in KRAS-Driven Cancers through Combined MEK Inhibition.

Hofmann, M.H.Gmachl, M.Ramharter, J.Savarese, F.Gerlach, D.Marszalek, J.R.Sanderson, M.P.Kessler, D.Trapani, F.Arnhof, H.Rumpel, K.Botesteanu, D.A.Ettmayer, P.Gerstberger, T.Kofink, C.Wunberg, T.Zoephel, A.Fu, S.C.Teh, J.L.Bottcher, J.Pototschnig, N.Schachinger, F.Schipany, K.Lieb, S.Vellano, C.P.O'Connell, J.C.Mendes, R.L.Moll, J.Petronczki, M.Heffernan, T.P.Pearson, M.McConnell, D.B.Kraut, N.

(2021) Cancer Discov 11: 142-157

  • DOI: https://doi.org/10.1158/2159-8290.CD-20-0142
  • Primary Citation Related Structures: 
    6SCM, 6SFR

  • PubMed Abstract: 

    KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancers. Direct KRAS blockade has proved challenging, and inhibition of a key downstream effector pathway, the RAF-MEK-ERK cascade, has shown limited success because of activation of feedback networks that keep the pathway in check. We hypothesized that inhibiting SOS1, a KRAS activator and important feedback node, represents an effective approach to treat KRAS-driven cancers. We report the discovery of a highly potent, selective, and orally bioavailable small-molecule SOS1 inhibitor, BI-3406, that binds to the catalytic domain of SOS1, thereby preventing the interaction with KRAS. BI-3406 reduces formation of GTP-loaded RAS and limits cellular proliferation of a broad range of KRAS-driven cancers. Importantly, BI-3406 attenuates feedback reactivation induced by MEK inhibitors and thereby enhances sensitivity of KRAS-dependent cancers to MEK inhibition. Combined SOS1 and MEK inhibition represents a novel and effective therapeutic concept to address KRAS-driven tumors. SIGNIFICANCE: To date, there are no effective targeted pan-KRAS therapies. In-depth characterization of BI-3406 activity and identification of MEK inhibitors as effective combination partners provide an attractive therapeutic concept for the majority of KRAS-mutant cancers, including those fueled by the most prevalent mutant KRAS oncoproteins, G12D, G12V, G12C, and G13D. See related commentary by Zhao et al., p. 17 . This article is highlighted in the In This Issue feature, p. 1 .


  • Organizational Affiliation
    • Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria. marco.hofmann@boehringer-ingelheim.com norbert.kraut@boehringer-ingelheim.com.

Macromolecule Content 

  • Total Structure Weight: 58.01 kDa 
  • Atom Count: 4,368 
  • Modeled Residue Count: 469 
  • Deposited Residue Count: 487 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L7H
(Subject of Investigation/LOI)

Query on L7H



Download:Ideal Coordinates CCD File
I [auth A]~{N}-[(1~{R})-1-[3-azanyl-5-(trifluoromethyl)phenyl]ethyl]-7-methoxy-2-methyl-6-[(3~{S})-oxolan-3-yl]oxy-quinazolin-4-amine
C23 H25 F3 N4 O3
XVFDNRYZXDHTHT-PXAZEXFGSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
L7H BindingDB:  6SCM Kd: min: 3, max: 470 (nM) from 3 assay(s)
IC50: min: 3, max: 1.00e+4 (nM) from 11 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.220 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.007α = 90
b = 78.74β = 90
c = 168.924γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2021-06-02
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references