7BIT

Inhibitor of MDM2-p53 Interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein-Protein Interaction.

Chessari, G.Hardcastle, I.R.Ahn, J.S.Anil, B.Anscombe, E.Bawn, R.H.Bevan, L.D.Blackburn, T.J.Buck, I.Cano, C.Carbain, B.Castro, J.Cons, B.Cully, S.J.Endicott, J.A.Fazal, L.Golding, B.T.Griffin, R.J.Haggerty, K.Harnor, S.J.Hearn, K.Hobson, S.Holvey, R.S.Howard, S.Jennings, C.E.Johnson, C.N.Lunec, J.Miller, D.C.Newell, D.R.Noble, M.E.M.Reeks, J.Revill, C.H.Riedinger, C.St Denis, J.D.Tamanini, E.Thomas, H.Thompson, N.T.Vinkovic, M.Wedge, S.R.Williams, P.A.Wilsher, N.E.Zhang, B.Zhao, Y.

(2021) J Med Chem 

  • DOI: 10.1021/acs.jmedchem.0c02188
  • Primary Citation of Related Structures:  
    7BIV, 7BJ0, 7BIT, 7BJ6, 7BIR, 7BMG

  • PubMed Abstract: 
  • Inhibition of murine double minute 2 (MDM2)-p53 protein-protein interaction with small molecules has been shown to reactivate p53 and inhibit tumor growth. Here, we describe rational, structure-guided, design of novel isoindolinone-based MDM2 inhibitors. MDM2 X-ray crystallography, quantum mechanics ligand-based design, and metabolite identification all contributed toward the discovery of potent in vitro and in vivo inhibitors of the MDM2-p53 interaction with representative compounds inducing cytostasis in an SJSA-1 osteosarcoma xenograft model following once-daily oral administration ...

    Inhibition of murine double minute 2 (MDM2)-p53 protein-protein interaction with small molecules has been shown to reactivate p53 and inhibit tumor growth. Here, we describe rational, structure-guided, design of novel isoindolinone-based MDM2 inhibitors. MDM2 X-ray crystallography, quantum mechanics ligand-based design, and metabolite identification all contributed toward the discovery of potent in vitro and in vivo inhibitors of the MDM2-p53 interaction with representative compounds inducing cytostasis in an SJSA-1 osteosarcoma xenograft model following once-daily oral administration.


    Organizational Affiliation

    Cancer Research UK Newcastle Drug Discovery Unit, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2,E3 ubiquitin-protein ligase Mdm2 A340Homo sapiensMutation(s): 2 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TV5
Query on TV5

Download Ideal Coordinates CCD File 
A
(3~{R})-2-[(5-chloranylpyridin-2-yl)methyl]-3-(4-chlorophenyl)-4-fluoranyl-3-[(1-oxidanylcyclopropyl)methoxy]-6-(2-oxidanylpropan-2-yl)isoindol-1-one
C27 H25 Cl2 F N2 O4
LAGWUKAFTJACQB-HHHXNRCGSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.022α = 90
b = 71.022β = 90
c = 101.194γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2021-01-13 
  • Released Date: 2021-04-07 
  • Deposition Author(s): Williams, P.A.

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release