4NYM

Approach for Targeting Ras with Small Molecules that Activate SOS-Mediated Nucleotide Exchange


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5529 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 111: 3401-3406

  • DOI: 10.1073/pnas.1315798111
  • Primary Citation of Related Structures:  
  • Also Cited By: 6D5V, 6D5M, 6D5L, 6D5J, 6D5H, 6D5G, 6D5E, 6D59, 6D56, 6D55, 6BVM, 6BVL, 6BVK, 6BVI

  • PubMed Abstract: 
  • Aberrant activation of the small GTPase Ras by oncogenic mutation or constitutively active upstream receptor tyrosine kinases results in the deregulation of cellular signals governing growth and survival in ∼30% of all human cancers. However, the dis ...

    Aberrant activation of the small GTPase Ras by oncogenic mutation or constitutively active upstream receptor tyrosine kinases results in the deregulation of cellular signals governing growth and survival in ∼30% of all human cancers. However, the discovery of potent inhibitors of Ras has been difficult to achieve. Here, we report the identification of small molecules that bind to a unique pocket on the Ras:Son of Sevenless (SOS):Ras complex, increase the rate of SOS-catalyzed nucleotide exchange in vitro, and modulate Ras signaling pathways in cells. X-ray crystallography of Ras:SOS:Ras in complex with these molecules reveals that the compounds bind in a hydrophobic pocket in the CDC25 domain of SOS adjacent to the Switch II region of Ras. The structure-activity relationships exhibited by these compounds can be rationalized on the basis of multiple X-ray cocrystal structures. Mutational analyses confirmed the functional relevance of this binding site and showed it to be essential for compound activity. These molecules increase Ras-GTP levels and disrupt MAPK and PI3K signaling in cells at low micromolar concentrations. These small molecules represent tools to study the acute activation of Ras and highlight a pocket on SOS that may be exploited to modulate Ras signaling.


    Organizational Affiliation

    Departments of Biochemistry, Pharmacology, and Chemistry, Vanderbilt University School of Medicine, Nashville, TN 37232.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase HRas
Q
166Homo 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
GTPase HRas
R
166Homo sapiensMutation(s): 0 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Son of sevenless homolog 1
S
481Homo sapiensMutation(s): 0 
Gene Names: SOS1
Find proteins for Q07889 (Homo sapiens)
Go to Gene View: SOS1
Go to UniProtKB:  Q07889
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RND
Query on RND

Download SDF File 
Download CCD File 
S
N-[1-(1H-indol-3-ylmethyl)piperidin-4-yl]-L-tryptophanamide
C25 H29 N5 O
YLGBZXMOCLUOKZ-QFIPXVFZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
Q
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
Q
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5529 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.158 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 186.805α = 90.00
b = 186.805β = 90.00
c = 178.684γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MAR345dtbdata collection
PHENIXrefinement
PHENIXmodel building
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references