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Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids.

Chee, S.M.Q., Wongsantichon, J., Siau, J., Thean, D., Ferrer, F., Robinson, R.C., Lane, D.P., Brown, C.J., Ghadessy, F.J.

(2017) PLoS ONE 12: e0189379-e0189379

  • DOI: 10.1371/journal.pone.0189379

  • PubMed Abstract: 

    • As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 t ...

    As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 tumour suppressor. Within this series, highest affinity was obtained by modification of an obligate tryptophan residue to the non-natural L-6-chlorotryptophan. To understand the structural basis for improved affinity we have solved the crystal structure of this stapled peptide (M011) bound to Mdm2 (residues 6-125) at 1.66 Å resolution. Surprisingly, near identity to the structure of a related peptide (M06) without the 6-chloro modification is observed. Further analysis of linear and stapled peptides comprising 6-Me-tryptophan provides mechanistic insight into dual Mdm2/Mdm4 antagonism and confirms L98 of Mdm4 as a mutable steric gate. The results also highlight a possible role of the flexible hinge region in determining Mdm2/Mdm4 plasticity.

    Organizational Affiliation: 

    Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore.,p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
122Homo sapiensMutation(s): 1 
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
Hydrocarbon stapled peptide THC-SER-PHE-0EH-GLU-TYR-6CW-ALA-LEU-LEU-MK8-NH2
C, D
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D
NON-POLYMERH2 N

--

6CW
Query on 6CW
C, D
L-PEPTIDE LINKINGC11 H11 Cl N2 O2TRP
THC
Query on THC
C, D
L-PEPTIDE LINKINGC6 H11 N O4THR
0EH
Query on 0EH
C, D
D-PEPTIDE LINKINGC10 H21 N O2

--

MK8
Query on MK8
C, D
L-peptide linkingC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.520α = 90.00
b = 106.410β = 90.00
c = 39.300γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
REFMACrefinement
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-04 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Brown, C.J.
Funding OrganizationLocationGrant Number
A-STARSingapore--

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release