4DSU

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity.

Maurer, T., Garrenton, L.S., Oh, A., Pitts, K., Anderson, D.J., Skelton, N.J., Fauber, B.P., Pan, B., Malek, S., Stokoe, D., Ludlam, M.J., Bowman, K.K., Wu, J., Giannetti, A.M., Starovasnik, M.A., Mellman, I., Jackson, P.K., Rudolph, J., Wang, W., Fang, G.

(2012) Proc Natl Acad Sci U S A 109: 5299-5304

  • DOI: 10.1073/pnas.1116510109
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an ...

    The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.

    Organizational Affiliation: 

    Structural Biology, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas, isoform 2BA189Homo sapiensMutation(s): 1 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS  P01116
GTEx  ENSG00000133703
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
BZI
Query on BZI
Download CCD File 
A
BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZIKd :  1500000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.553α = 90
b = 79.553β = 90
c = 78.055γ = 120
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2012-06-06
    Changes: Database references