5EXA

Small-molecule stabilization of the 14-3-3/Gab2 PPI interface

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Small-Molecule Stabilization of the 14-3-3/Gab2 Protein-Protein Interaction (PPI) Interface.

Bier, D., Bartel, M., Sies, K., Halbach, S., Higuchi, Y., Haranosono, Y., Brummer, T., Kato, N., Ottmann, C.

(2016) ChemMedChem 11: 911-918

  • DOI: 10.1002/cmdc.201500484
  • Primary Citation of Related Structures:  
    5EXA, 5EWZ

  • PubMed Abstract: 

    • Small-molecule modulation of protein-protein interactions (PPIs) is one of the most promising new areas in drug discovery. In the vast majority of cases only inhibition or disruption of PPIs is realized, whereas the complementary strategy of targeted ...

    Small-molecule modulation of protein-protein interactions (PPIs) is one of the most promising new areas in drug discovery. In the vast majority of cases only inhibition or disruption of PPIs is realized, whereas the complementary strategy of targeted stabilization of PPIs is clearly under-represented. Here, we report the example of a semi-synthetic natural product derivative--ISIR-005--that stabilizes the cancer-relevant interaction of the adaptor protein 14-3-3 and Gab2. The crystal structure of ISIR-005 in complex with 14-3-3 and the binding motif of Gab2 comprising two phosphorylation sites (Gab2pS210pT391) showed how the stabilizing molecule binds to the rim-of-the-interface of the protein complex. Only in the direct vicinity of 14-3-3/Gab2pT391 site is a pre-formed pocket occupied by ISIR-005; binding of the Gab2pS210 motif to 14-3-3 does not create an interface pocket suitable for the molecule. Accordingly, ISIR-005 only stabilizes the binding of the Gab2pT391 but not the Gab2pS210 site. This study represents structural and biochemical proof of the druggability of the 14-3-3/Gab2 PPI interface with important implications for the development of PPI stabilizers.

    Organizational Affiliation: 

    Department of Biomedical Engineering, Institute for Complex Molecular, Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands. christian.ottmann@uni-due.de, c.ottmann@tue.nl.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein zeta/deltaA, B230Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Explore P63104 
Go to UniProtKB:  P63104
NIH Common Fund Data Resources
PHAROS  P63104
GTEx  ENSG00000164924
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GRB2-associated-binding protein 2C, D11Homo sapiensMutation(s): 0 
Gene Names: GAB2, KIAA0571
Find proteins for Q9UQC2 (Homo sapiens)
Explore Q9UQC2 
Go to UniProtKB:  Q9UQC2
NIH Common Fund Data Resources
PHAROS  Q9UQC2
GTEx  ENSG00000033327
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SO
Query on 5SO
Download Ideal Coordinates CCD File 
A, B
Fusicoccin A-THF derivative
C30 H48 O8
LOAPHXVWCJVEPY-FNWYVXGSSA-N		 Ligand Interaction
BEZ
Query on BEZ
Download Ideal Coordinates CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		C,DL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72α = 90
b = 83.09β = 90
c = 111.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-11-23 
  • Released Date: 2016-05-04 
    • Deposition Author(s): Bier, D., Ottmann, C.

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Derived calculations