Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18223.92 
• Atom Count: 1206 
• Residue Count: 152 
• Unique protein chains: 1

4JVF

The Crystal structure of PDE6D in complex with the inhibitor (s)-5

• DOI: 10.2210/pdb4JVF/pdb

• Classification: Protein binding/inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-03-25 Released: 2013-05-22 
• Deposition Author(s): Gunther, Z., Papke, B., Ismail, S., Vartak, N., Chandra, A., Hoffmann, M., Hahn, S., Triola, G., Wittinghofer, A., Bastiaens, P., Waldmann, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.257 
• R-Value Work: 0.207 

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

• PubMed: 23698361 
• DOI: 10.1038/nature12205
• Primary Citation of Related Structures:  
  4JVB, 4JV8, 4JV6


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	B	152	Homo sapiens	Mutation(s): 0  Gene Names: PDE6D (PDED)
Find proteins for O43924 (Homo sapiens) Go to Gene View: PDE6D Go to UniProtKB:  O43924

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
17X	B	(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate C40 H42 N6 O2 WDALFJYWTFDSRP-DIPNUNPCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
17X	Kd: 0.1 - 10 nM (100) BINDINGDB
17X	Kd: 10 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.257 
• R-Value Work: 0.207 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 55.910	α = 90.00
b = 55.910	β = 90.00
c = 116.670	γ = 120.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
ProDC	data collection
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-25 
• Released Date: 2013-05-22 
• Deposition Author(s): Gunther, Z., Papke, B., Ismail, S., Vartak, N., Chandra, A., Hoffmann, M., Hahn, S., Triola, G., Wittinghofer, A., Bastiaens, P., Waldmann, H.

Revision History 

• Version 1.0: 2013-05-22
  Type: Initial release
• Version 1.1: 2013-06-05
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description