6D5L

Ras:SOS:Ras in complex with a small molecule activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS.

Hodges, T.R.Abbott, J.R.Little, A.J.Sarkar, D.Salovich, J.M.Howes, J.E.Akan, D.T.Sai, J.Arnold, A.L.Browning, C.Burns, M.C.Sobolik, T.Sun, Q.Beesetty, Y.Coker, J.A.Scharn, D.Stadtmueller, H.Rossanese, O.W.Phan, J.Waterson, A.G.McConnell, D.B.Fesik, S.W.

(2018) J. Med. Chem. 61: 8875-8894

  • DOI: 10.1021/acs.jmedchem.8b01108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involve ...

    Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.


    Related Citations: 
    • Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
      Burns, M.C.,Sun, Q.,Daniels, R.N.,Camper, D.,Kennedy, J.P.,Phan, J.,Olejniczak, E.T.,Lee, T.,Waterson, A.G.,Rossanese, O.W.,Fesik, S.W.
      (2014) Proc. Natl. Acad. Sci. U.S.A. 111: 3401


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.,Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase HRas
A
167Homo sapiensMutation(s): 0 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Son of sevenless homolog 1
B
482Homo sapiensMutation(s): 0 
Gene Names: SOS1
Find proteins for Q07889 (Homo sapiens)
Go to Gene View: SOS1
Go to UniProtKB:  Q07889
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
GTPase HRas
C
167Homo sapiensMutation(s): 0 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FW7
Query on FW7

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B
6-chloro-1-[(3-chloro-4-fluorophenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
C18 H17 Cl2 F N4
JKACBCFXETVIIK-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A, B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.159 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 183.757α = 90.00
b = 183.757β = 90.00
c = 178.445γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesLustgarten

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references