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 

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:  

  • 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

    Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.,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.,Institute of Molecular Medicine & Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany. tilman.brummer@mail.zbsa.uni-freiburg.de.,Department of Biomedical Engineering, Institute for Complex Molecular, Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Spemann Graduate School of Biology & Medicine, University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany.,Institute of Molecular Medicine & Cell Research (IMMZ), Faculty of Medicine, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg, Germany.,BIOSS: Centre for Biological Signaling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany. tilman.brummer@mail.zbsa.uni-freiburg.de.,The Institute of Scientific & Industrial Research, Osaka University, Osaka, 567-0047, Japan. kato-n@sanken.osaka-u.ac.jp.,Department of Chemistry, University of Duisburg-Essen, Universitätstr. 7, 45141, Essen, Germany.,The Institute of Scientific & Industrial Research, Osaka University, Osaka, 567-0047, Japan.,Department of Chemistry, University of Duisburg-Essen, Universitätstr. 7, 45141, Essen, Germany. christian.ottmann@uni-due.de, c.ottmann@tue.nl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein zeta/delta
A, B
230Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Go to Gene View: YWHAZ
Go to UniProtKB:  P63104
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GRB2-associated-binding protein 2
C, D
11Homo sapiensMutation(s): 0 
Gene Names: GAB2 (KIAA0571)
Find proteins for Q9UQC2 (Homo sapiens)
Go to Gene View: GAB2
Go to UniProtKB:  Q9UQC2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SO
Query on 5SO

Download SDF File 
Download CCD File 
A, B
Fusicoccin A-THF derivative
C30 H48 O8
LOAPHXVWCJVEPY-FNWYVXGSSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
C, D
L-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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.000α = 90.00
b = 83.090β = 90.00
c = 111.150γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Derived calculations