6RJL

Fragment AZ-018 binding at the TAZpS89/14-3-3 sigma interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6SIN 6SLX


Literature

Fragment-based Differential Targeting of PPI Stabilizer Interfaces.

Guillory, X.Wolter, M.Leysen, S.Neves, J.F.Kuusk, A.Genet, S.Somsen, B.Morrow, J.K.Rivers, E.van Beek, L.Patel, J.Goodnow, R.Schoenherr, H.Fuller, N.Cao, Q.Doveston, R.G.Brunsveld, L.Arkin, M.R.Castaldi, P.Boyd, H.Landrieu, I.Chen, H.Ottmann, C.

(2020) J Med Chem 63: 6694-6707

  • DOI: 10.1021/acs.jmedchem.9b01942
  • Primary Citation of Related Structures:  
    6RWS, 6RWU, 6RX2, 6RWH, 6RWI, 6S9Q, 6SIO, 6SIN, 6SIQ, 6SIP

  • PubMed Abstract: 
  • Stabilization of protein-protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question ...

    Stabilization of protein-protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question. We report here how a fragment-based approach can be used to identify chemical starting points for the development of small-molecule stabilizers that differentiate between two different PPI interfaces of the adapter protein 14-3-3. The fragments discriminately bind to the interface of 14-3-3 with the recognition motif of either the tumor suppressor protein p53 or the oncogenic transcription factor TAZ. This X-ray crystallography driven study shows that the rim of the interface of individual 14-3-3 complexes can be targeted in a differential manner with fragments that represent promising starting points for the development of specific 14-3-3 PPI stabilizers.


    Organizational Affiliation

    Department of Organic Chemistry, University of Duisburg-Essen, 47057 Duisburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein sigmaA253Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TAZpS89B [auth P]13Homo sapiensMutation(s): 0 
Gene Names: WWTR1TAZ
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZV5 (Homo sapiens)
Explore Q9GZV5 
Go to UniProtKB:  Q9GZV5
PHAROS:  Q9GZV5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K5Z
Query on K5Z

Download Ideal Coordinates CCD File 
C [auth P]5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide
C14 H17 N3 S
MCPMDVYDZQBIHS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B [auth P]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.2α = 90
b = 112.39β = 90
c = 62.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionNetherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references