6CUO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS.

Abbott, J.R.Patel, P.A.Howes, J.E.Akan, D.T.Kennedy, J.P.Burns, M.C.Browning, C.F.Sun, Q.Rossanese, O.W.Phan, J.Waterson, A.G.Fesik, S.W.

(2018) ACS Med Chem Lett 9: 941-946

  • DOI: 10.1021/acsmedchemlett.8b00296
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One appro ...

    Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway.


    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 Biochemistry and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.,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
NA
Query on NA

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

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Download CCD File 
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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Download CCD File 
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
FFS
Query on FFS

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Download CCD File 
B
N~2~-(3-chlorophenyl)-N~4~-[(furan-2-yl)methyl]quinazoline-2,4-diamine
C19 H15 Cl N4 O
KLRNKMZSARWWTH-UHFFFAOYSA-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: 1.73 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.164 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 183.806α = 90.00
b = 183.806β = 90.00
c = 178.872γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

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: 2019-02-06
    Type: Initial release