6RHC

Fragment AZ-003 binding at the TAZpS89/14-3-3 sigma interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Re-refinement Note

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


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: https://doi.org/10.1021/acs.jmedchem.9b01942
  • Primary Citation of Related Structures:  
    6R5L, 6RHC, 6RJL, 6RJQ, 6RJZ, 6RK8, 6RKI, 6RKK, 6RKM, 6RL3, 6RL4, 6RL6, 6RM5, 6RM7, 6RP6, 6RWH, 6RWI, 6RWS, 6RWU, 6RX2, 6S39, 6S3C, 6S40, 6S9Q, 6SIN, 6SIO, 6SIP, 6SIQ, 6SLV, 6SLW, 6SLX

  • 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. 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

    CNRS ERL9002 Integrative Structural Biology F-59000 Lille, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo 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
GTEx:  ENSG00000175793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WW domain-containing transcription regulator protein 1B [auth P]13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZV5 (Homo sapiens)
Explore Q9GZV5 
Go to UniProtKB:  Q9GZV5
PHAROS:  Q9GZV5
GTEx:  ENSG00000018408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZV5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.025α = 90
b = 112.307β = 90
c = 62.697γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description