4LWT | pdb_00004lwt

The 1.6A Crystal Structure of Humanized Xenopus MDM2 with RO5027344


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.247 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.222 (Depositor) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4LWT

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of potent and selective spiroindolinone MDM2 inhibitor, RO8994, for cancer therapy.

Zhang, Z.Ding, Q.Liu, J.J.Zhang, J.Jiang, N.Chu, X.J.Bartkovitz, D.Luk, K.C.Janson, C.Tovar, C.Filipovic, Z.M.Higgins, B.Glenn, K.Packman, K.Vassilev, L.T.Graves, B.

(2014) Bioorg Med Chem 22: 4001-4009

  • DOI: https://doi.org/10.1016/j.bmc.2014.05.072
  • Primary Citation Related Structures: 
    4LWT, 4LWU

  • PubMed Abstract: 

    The field of small-molecule inhibitors of protein-protein interactions is rapidly advancing and the specific area of inhibitors of the p53/MDM2 interaction is a prime example. Several groups have published on this topic and multiple compounds are in various stages of clinical development. Building on the strength of the discovery of RG7112, a Nutlin imidazoline-based compound, and RG7388, a pyrrolidine-based compound, we have developed additional scaffolds that provide opportunities for future development. Here, we report the discovery and optimization of a highly potent and selective series of spiroindolinone small-molecule MDM2 inhibitors, culminating in RO8994.


  • Organizational Affiliation
    • Discovery Chemistry, Roche Research Center, Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07110, United States. Electronic address: zzhang85@its.jnj.com.

Macromolecule Content 

  • Total Structure Weight: 10.48 kDa 
  • Atom Count: 854 
  • Modeled Residue Count: 86 
  • Deposited Residue Count: 86 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm286Xenopus laevisMutation(s): 3 
Gene Names: mdm2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for P56273 (Xenopus laevis)
Explore P56273 
Go to UniProtKB:  P56273
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56273
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
20Q

Query on 20Q



Download:Ideal Coordinates CCD File
B [auth A](3S)-3-[(3R)-1-acetylpiperidin-3-yl]-6-chloro-3-(3-chlorobenzyl)-1,3-dihydro-2H-indol-2-one
C22 H22 Cl2 N2 O2
RIBYLXUNNWIWJK-AOMKIAJQSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.247 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.222 (Depositor) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.066α = 90
b = 67.976β = 90
c = 67.168γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations