6BVL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.748 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling.

Abbott, J.R.Hodges, T.R.Daniels, R.N.Patel, P.A.Kennedy, J.P.Howes, J.E.Akan, D.T.Burns, M.C.Sai, J.Sobolik, T.Beesetty, Y.Lee, T.Rossanese, O.W.Phan, J.Waterson, A.G.Fesik, S.W.

(2018) J. Med. Chem. 61: 6002-6017

  • DOI: 10.1021/acs.jmedchem.8b00360
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS ...

    Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2 T202/Y204 protein levels at higher compound concentrations.


    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

    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): 1 
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
EBY
Query on EBY

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Download CCD File 
B
N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-5-methyl-L-tryptophanamide
C26 H30 Cl N5 O
ORZWUMKDZDLNTJ-QHCPKHFHSA-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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B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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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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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: 1.748 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.157 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 184.209α = 90.00
b = 184.209β = 90.00
c = 179.093γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Lustgarden FoundationUnited States--

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references
  • Version 1.2: 2019-05-29
    Type: Data collection