5XXK

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 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    5XXK

  • 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

    p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2AB122Homo sapiensMutation(s): 1 
Gene Names: MDM2
EC: 2.3.2.27
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
Hydrocarbon stapled peptide THC-SER-PHE-0EH-GLU-TYR-6CW-ALA-LEU-LEU-MK8-NH2CD12Phage display vector pTDispMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
6CW
Query on 6CW
C,DL-PEPTIDE LINKINGC11 H11 Cl N2 O2TRP
MK8
Query on MK8
C,DL-PEPTIDE LINKINGC7 H15 N O2LEU
THC
Query on THC
C,DL-PEPTIDE LINKINGC6 H11 N O4THR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.52α = 90
b = 106.41β = 90
c = 39.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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