5AFG

Structure of the Stapled Peptide Bound to Mdm2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 

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

  • 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 s ...

    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).,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA (UK).,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551.,Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK).,p53Lab, A*STAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648 (Singapore).,Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW (UK). spring@ch.cam.ac.uk.,Hutchison/MRC Research Centre, Hills Rd, Cambridge CB2 0XZ (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE MDM2
A
97Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
STAPLED PEPTIDE
B
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P07
Query on P07

Download SDF File 
Download CCD File 
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
B
L-PEPTIDE LINKINGC8 H15 N O3LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.176 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 36.821α = 90.00
b = 36.821β = 90.00
c = 177.416γ = 90.00
Software Package:
Software NamePurpose
PROTEUM2data reduction
PROTEUM2data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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