5AFG

Structure of the Stapled Peptide Bound to Mdm2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Double Strain-Promoted Macrocyclization for the Rapid Selection of Cell-Active Stapled Peptides.

Lau, Y.H.Wu, Y.Rossmann, M.Tan, B.X.De Andrade, P.Tan, Y.S.Verma, C.Mckenzie, G.J.Venkitaraman, A.R.Hyvonen, M.Spring, D.R.

(2015) Angew Chem Int Ed Engl 54: 15410

  • DOI: https://doi.org/10.1002/anie.201508416
  • Primary Citation of Related Structures:  
    5AFG

  • PubMed Abstract: 

    Peptide stapling is a method for designing macrocyclic alpha-helical inhibitors of protein-protein interactions. However, obtaining a cell-active inhibitor can require significant optimization. We report a novel stapling technique based on a double strain-promoted azide-alkyne reaction, and exploit its biocompatibility to accelerate the discovery of cell-active stapled peptides. As a proof of concept, MDM2-binding peptides were stapled in parallel, directly in cell culture medium in 96-well plates, and simultaneously evaluated in a p53 reporter assay. This in situ stapling/screening process gave an optimal candidate that showed improved proteolytic stability and nanomolar binding to MDM2 in subsequent biophysical assays. α-Helicity was confirmed by a crystal structure of the MDM2-peptide complex. This work introduces in situ stapling as a versatile biocompatible technique with many other potential high-throughput biological applications.


  • Organizational Affiliation

    Bioinformatics Institute, A*STAR, 30 Biopolis St, #07-01 Matrix, Singapore 138671 (Singapore).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE MDM297Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
STAPLED PEPTIDE12synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P07
Query on P07

Download Ideal Coordinates CCD File 
C [auth B]1,8-DIETHYL-1,8-DIHYDRODIBENZO[3,4:7,8][1,2,3]TRIAZOLO[4',5':5,6]CYCLOOCTA[1,2-D][1,2,3]TRIAZOLE
C20 H18 N6
YRZRZRBFIALCLI-MKVCYXFSSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LAY
Query on LAY
B
L-PEPTIDE LINKINGC8 H15 N O3LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.821α = 90
b = 36.821β = 90
c = 177.416γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 2.0: 2019-05-15
    Changes: Data collection, Derived calculations, Other, Polymer sequence