6D59

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.8b01108
  • Primary Citation of Related Structures:  
    6D55, 6D56, 6D59, 6D5E, 6D5G, 6D5H, 6D5J, 6D5L, 6D5M, 6D5V, 6D5W

  • 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 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.


  • Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRas167Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1482Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRas167Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FVJ
Query on FVJ

Download Ideal Coordinates CCD File 
F [auth B]6-chloro-4-(3,5-dimethyl-1H-pyrazol-4-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
C25 H28 Cl F N6
SVULJAPKAMXBBJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth C]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
FVJ BindingDB:  6D59 Kd: 100 (nM) from 1 assay(s)
EC50: min: 9000, max: 1.56e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.107α = 90
b = 184.107β = 90
c = 179.426γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesLustgarten

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection