4URX

The crystal structure of H-Ras and SOS in complex with ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small Molecule Binding Sites on the Ras:SOS Complex Can be Exploited for Inhibition of Ras Activation.

Winter, J.Anderson, M.Blades, K.Chresta, C.Embrey, K.J.Fairley, G.Faulder, P.Finlay, M.R.V.Kettle, J.G.Nowak, T.Overman, R.Patel, S.J.Perkins, P.Spadola, L.Tart, J.Tucker, J.A.Wrigley, G.

(2015) J Med Chem 58: 2265

  • DOI: 10.1021/jm501660t
  • Primary Citation of Related Structures:  
    4US0, 4US1, 4URY, 4URZ, 4US2, 4URU, 4URV, 4URW, 4URX

  • PubMed Abstract: 
  • Constitutively active mutant KRas displays a reduced rate of GTP hydrolysis via both intrinsic and GTPase-activating protein-catalyzed mechanisms, resulting in the perpetual activation of Ras pathways. We describe a fragment screening campaign using ...

    Constitutively active mutant KRas displays a reduced rate of GTP hydrolysis via both intrinsic and GTPase-activating protein-catalyzed mechanisms, resulting in the perpetual activation of Ras pathways. We describe a fragment screening campaign using X-ray crystallography that led to the discovery of three fragment binding sites on the Ras:SOS complex. The identification of tool compounds binding at each of these sites allowed exploration of two new approaches to Ras pathway inhibition by stabilizing or covalently modifying the Ras:SOS complex to prevent the reloading of Ras with GTP. Initially, we identified ligands that bound reversibly to the Ras:SOS complex in two distinct sites, but these compounds were not sufficiently potent inhibitors to validate our stabilization hypothesis. We conclude by demonstrating that covalent modification of Cys118 on Ras leads to a novel mechanism of inhibition of the SOS-mediated interaction between Ras and Raf and is effective at inhibiting the exchange of labeled GDP in both mutant (G12C and G12V) and wild type Ras.


    Organizational Affiliation

    AstraZeneca , Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPASE HRASR185Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS  P01112
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SON OF SEVENLESS HOMOLOG 1S487Homo sapiensMutation(s): 0 
Gene Names: SOS1
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
NIH Common Fund Data Resources
PHAROS  Q07889
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HXY
Query on HXY

Download CCD File 
S
1-(4-bromobenzyl)pyrrolidine
C11 H14 Br N
UKJIGXJYXLVARZ-UHFFFAOYSA-N
 Ligand Interaction
FK1
Query on FK1

Download CCD File 
S
6-bromo-1H-indole
C8 H6 Br N
MAWGHOPSCKCTPA-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
S
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FK1Kd:  6000000   nM  Binding MOAD
HXYKd:  1300000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.874α = 90
b = 149.874β = 90
c = 199.701γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references