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 

wwPDB Validation   3D Report Full Report


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: 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 ...

    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

    Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK). spring@ch.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE MDM2A97Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS:  Q00987
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
STAPLED PEPTIDEB12synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LAY
Query on LAY
BL-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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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