7THL

Structure of mouse double minute 2 homolog (MDM2) RING domain in complex with Inulanolide A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Literature

Structural studies of antitumor compounds that target the RING domain of MDM2.

Terrell, J.R.Tang, S.Faniyi, O.O.Jeong, I.H.Yin, J.Nijampatnam, B.Velu, S.E.Wang, W.Zhang, R.Luo, M.

(2022) Protein Sci 31: e4367-e4367

  • DOI: 10.1002/pro.4367
  • Primary Citation of Related Structures:  
    7T59, 7TFG, 7THL

  • PubMed Abstract: 
  • Mouse double minute 2 homolog (MDM2) is an E3 ubiquitin-protein ligase that is involved in the transfer of ubiquitin to p53 and other protein substrates. The expression of MDM2 is elevated in cancer cells and inhibitors of MDM2 showed potent anticancer activities ...

    Mouse double minute 2 homolog (MDM2) is an E3 ubiquitin-protein ligase that is involved in the transfer of ubiquitin to p53 and other protein substrates. The expression of MDM2 is elevated in cancer cells and inhibitors of MDM2 showed potent anticancer activities. Many inhibitors target the p53 binding domain of MDM2. However, inhibitors such as Inulanolide A and MA242 are found to bind the RING domain of MDM2 to block ubiquitin transfer. In this report, crystal structures of MDM2 RING domain in complex with Inulanolide A and MA242 were solved. These inhibitors primarily bind in a hydrophobic site centered at the sidechain of Tyr489 at the C-terminus of MDM2 RING domain. The C-terminus of MDM2 RING domain, especially residue Tyr489, is required for ubiquitin discharge induced by MDM2. The binding of these inhibitors at Tyr489 may interrupt interactions between the MDM2 RING domain and the E2-Ubiquitin complex to inhibit ubiquitin transfer, regardless of what the substrate is. Our results suggest a new mechanism of inhibition of MDM2 E3 activity for a broad spectrum of substrates.


    Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A, B, C, D68FelisMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
UniProt
Find proteins for Q7YRZ8 (Felis catus)
Explore Q7YRZ8 
Go to UniProtKB:  Q7YRZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7YRZ8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.145α = 90
b = 39.618β = 94.11
c = 102.656γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA214019

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release