5LAY

Discovery of New Natural-product-inspired Spiro-oxindole Compounds as Orally Active Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 6g


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of Novel Spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-one Compounds as Chemically Stable and Orally Active Inhibitors of the MDM2-p53 Interaction.

Gollner, A.Rudolph, D.Arnhof, H.Bauer, M.Blake, S.M.Boehmelt, G.Cockroft, X.L.Dahmann, G.Ettmayer, P.Gerstberger, T.Karolyi-Oezguer, J.Kessler, D.Kofink, C.Ramharter, J.Rinnenthal, J.Savchenko, A.Schnitzer, R.Weinstabl, H.Weyer-Czernilofsky, U.Wunberg, T.McConnell, D.B.

(2016) J. Med. Chem. 59: 10147-10162

  • DOI: 10.1021/acs.jmedchem.6b00900
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Scaffold modification based on Wang's pioneering MDM2-p53 inhibitors led to novel, chemically stable spiro-oxindole compounds bearing a spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-one scaffold that are not prone to epimerization as observed for the initia ...

    Scaffold modification based on Wang's pioneering MDM2-p53 inhibitors led to novel, chemically stable spiro-oxindole compounds bearing a spiro[3H-indole-3,2'-pyrrolidin]-2(1H)-one scaffold that are not prone to epimerization as observed for the initial spiro[3H-indole-3,3'-pyrrolidin]-2(1H)-one scaffold. Further structure-based optimization inspired by natural product architectures led to a complex fused ring system ideally suited to bind to the MDM2 protein and to interrupt its protein-protein interaction (PPI) with TP53. The compounds are highly selective and show in vivo efficacy in a SJSA-1 xenograft model even when given as a single dose as demonstrated for 4-[(3S,3'S,3'aS,5'R,6'aS)-6-chloro-3'-(3-chloro-2-fluorophenyl)-1'-(cyclopropylmethyl)-2-oxo-1,2,3',3'a,4',5',6',6'a-octahydro-1'H-spiro[indole-3,2'-pyrrolo[3,2-b]pyrrole]-5'-yl]benzoic acid (BI-0252).


    Organizational Affiliation

    Boehringer Ingelheim RCV GmbH & Co. KG , Dr. Boehringer-Gasse 5-11, A-1121 Vienna, Austria.,Boehringer Ingelheim Pharma GmbH & Co. KG , 88400 Biberach, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B, C, D, E, F
95Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6SS
Query on 6SS

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one
C27 H26 Cl2 F N3 O2
VTZPRLPCZBTKSH-VFICKSILSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.251 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.450α = 90.00
b = 71.450β = 90.00
c = 520.977γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2019-06-12
    Type: Advisory, Data collection, Structure summary