7BIV

Inhibitor of MDM2-p53 Interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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 64: 4071-4088

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


  • Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm298Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TUW (Subject of Investigation/LOI)
Query on TUW

Download Ideal Coordinates CCD File 
G [auth A]6-[[(1~{R})-1-(4-chlorophenyl)-7-fluoranyl-1-[[1-(hydroxymethyl)cyclopropyl]methoxy]-3-oxidanylidene-5-(2-oxidanylpropan-2-yl)isoindol-2-yl]methyl]pyridine-3-carbonitrile
C29 H27 Cl F N3 O4
GDVBWGYVVZIZIR-GDLZYMKVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.646α = 90
b = 71.646β = 90
c = 100.483γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
pointlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 2.0: 2021-04-21
    Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary