4JVB

Crystal structure of PDE6D in complex with the inhibitor rac-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling

Zimmermann, G.Papke, B.Ismail, S.Vartak, N.Chandra, A.Hoffmann, M.Hahn, S.A.Triola, G.Wittinghofer, A.Bastiaens, P.I.Waldmann, H.

(2013) Nature 497: 638-642

  • DOI: 10.1038/nature12205
  • Primary Citation of Related Structures:  4JV6, 4JV8, 4JVF

  • PubMed Abstract: 
  • The KRAS oncogene product is considered a major target in anticancer drug discovery. However, direct interference with KRAS signalling has not yet led to clinically useful drugs. Correct localization and signalling by farnesylated KRAS is regulated b ...

    The KRAS oncogene product is considered a major target in anticancer drug discovery. However, direct interference with KRAS signalling has not yet led to clinically useful drugs. Correct localization and signalling by farnesylated KRAS is regulated by the prenyl-binding protein PDEδ, which sustains the spatial organization of KRAS by facilitating its diffusion in the cytoplasm. Here we report that interfering with binding of mammalian PDEδ to KRAS by means of small molecules provides a novel opportunity to suppress oncogenic RAS signalling by altering its localization to endomembranes. Biochemical screening and subsequent structure-based hit optimization yielded inhibitors of the KRAS-PDEδ interaction that selectively bind to the prenyl-binding pocket of PDEδ with nanomolar affinity, inhibit oncogenic RAS signalling and suppress in vitro and in vivo proliferation of human pancreatic ductal adenocarcinoma cells that are dependent on oncogenic KRAS. Our findings may inspire novel drug discovery efforts aimed at the development of drugs targeting oncogenic RAS.


    Organizational Affiliation

    Department of Chemical Biology, Max Planck Institute of Molecular Physiology, D-44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
B
152Homo sapiensGene Names: PDE6D (PDED)
Find proteins for O43924 (Homo sapiens)
Go to Gene View: PDE6D
Go to UniProtKB:  O43924
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1M0
Query on 1M0

Download SDF File 
Download CCD File 
B
1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
C38 H32 N4 O
VETKHSOXOHNPCG-WJOKGBTCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1M0Kd: 39 nM BINDINGMOAD
1M0Kd: 39 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.680α = 90.00
b = 55.680β = 90.00
c = 116.550γ = 120.00
Software Package:
Software NamePurpose
PROdata collection
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references