4UMN

Structure of a stapled peptide antagonist bound to Nutlin-resistant Mdm2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a stapled peptide antagonist bound to nutlin-resistant Mdm2.

Chee, S.M.Wongsantichon, J.Soo Tng, Q.Robinson, R.Joseph, T.L.Verma, C.Lane, D.P.Brown, C.J.Ghadessy, F.J.

(2014) PLoS ONE 9: e104914-e104914

  • DOI: 10.1371/journal.pone.0104914

  • PubMed Abstract: 
  • As key negative regulator of the p53 tumour suppressor, Mdm2 is an attractive therapeutic target. Small molecules such as Nutlin have been developed to antagonise Mdm2, resulting in p53-dependent death of tumour cells. We have recently described a mu ...

    As key negative regulator of the p53 tumour suppressor, Mdm2 is an attractive therapeutic target. Small molecules such as Nutlin have been developed to antagonise Mdm2, resulting in p53-dependent death of tumour cells. We have recently described a mutation in Mdm2 (M62A), which precludes binding of Nutlin, but not p53. This Nutlin-resistant variant is not, however, refractory to binding and inhibition by stapled peptide antagonists targeting the same region of Mdm2. A detailed understanding of how stapled peptides are recalcitrant to Mdm2 mutations conferring Nutlin-resistance will aid in the further development of potent Mdm2 antagonists. Here, we report the 2.00 Å crystal structure of a stapled peptide antagonist bound to Nutlin resistant Mdm2. The stapled peptide relies on an extended network of interactions along the hydrophobic binding cleft of Mdm2 for high affinity binding. Additionally, as seen in other stapled peptide structures, the hydrocarbon staple itself contributes to binding through favourable interactions with Mdm2. The structure highlights the intrinsic plasticity present in both Mdm2 and the hydrocarbon staple moiety, and can be used to guide future iterations of both small molecules and stapled peptides for improved antagonists of Mdm2.


    Organizational Affiliation

    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
120Homo 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
M06
C, D
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
NME
Query on NME
C, D
NON-POLYMERC H5 N

--

0EH
Query on 0EH
C, D
D-PEPTIDE LINKINGC10 H21 N O2

--

MK8
Query on MK8
C, D
L-peptide linkingC7 H15 N O2LEU
ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.076α = 90.00
b = 65.674β = 90.00
c = 105.683γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Atomic model, Other
  • Version 1.2: 2014-08-27
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Database references