6Q2X | pdb_00006q2x

TEAD4 (216-434) COMPLEXED WITH YAP PEPTIDE (60-100) AND MYRISTOATE (COVALENTLY BOUND) AT 2.1A (P41212 CRYSTAL FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.253 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.232 (Depositor) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Q2X

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence.

Furet, P.Salem, B.Mesrouze, Y.Schmelzle, T.Lewis, I.Kallen, J.Chene, P.

(2019) Bioorg Med Chem Lett 29: 2316-2319

  • DOI: https://doi.org/10.1016/j.bmcl.2019.06.022
  • Primary Citation Related Structures: 
    6Q2X, 6Q36

  • PubMed Abstract: 

    The YAP-TEAD protein-protein interaction is a potential therapeutic target to treat cancers in which the Hippo signaling pathway is deregulated. However, the extremely large surface of interaction between the two proteins presents a formidable challenge for a small molecule interaction disrupter approach. We have accomplished progress towards showing the feasibility of this approach by the identification of a 15-mer peptide able to potently (nanomolar range) disrupt the YAP-TEAD interaction by targeting only one of the two important sites of interaction. This peptide, incorporating non-natural amino acids selected by structure-based design, is derived from the Ω-loop sequence 85-99 of YAP.


  • Organizational Affiliation
    • Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. Electronic address: pascal.furet@novartis.com.

Macromolecule Content 

  • Total Structure Weight: 30.57 kDa 
  • Atom Count: 2,149 
  • Modeled Residue Count: 243 
  • Deposited Residue Count: 261 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-3220Homo sapiensMutation(s): 0 
Gene Names: TEAD4RTEF1TCF13L1TEF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15561 (Homo sapiens)
Explore Q15561 
Go to UniProtKB:  Q15561
PHAROS:  Q15561
GTEx:  ENSG00000197905 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15561
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional coactivator YAP1B [auth L]41Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P46937 (Homo sapiens)
Explore P46937 
Go to UniProtKB:  P46937
PHAROS:  P46937
GTEx:  ENSG00000137693 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46937
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.253 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.232 (Depositor) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.096α = 90
b = 59.096β = 90
c = 158.949γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2019-07-03 
  • Deposition Author(s): Kallen, J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary