4J3E

The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of RG7112: A Small-Molecule MDM2 Inhibitor in Clinical Development.

Vu, B.Wovkulich, P.Pizzolato, G.Lovey, A.Ding, Q.Jiang, N.Liu, J.J.Zhao, C.Glenn, K.Wen, Y.Tovar, C.Packman, K.Vassilev, L.Graves, B.

(2013) ACS Med Chem Lett 4: 466-469

  • DOI: 10.1021/ml4000657

  • PubMed Abstract: 
  • The p53 tumor suppressor is a potent transcription factor that plays a key role in the regulation of cellular responses to stress. It is controlled by its negative regulator MDM2, which binds directly to p53 and inhibits its transcriptional activity. ...

    The p53 tumor suppressor is a potent transcription factor that plays a key role in the regulation of cellular responses to stress. It is controlled by its negative regulator MDM2, which binds directly to p53 and inhibits its transcriptional activity. MDM2 also targets p53 for degradation by the proteasome. Many tumors produce high levels of MDM2, thereby impairing p53 function. Restoration of p53 activity by inhibiting the p53-MDM2 interaction may represent a novel approach to cancer treatment. RG7112 (2g) is the first clinical small-molecule MDM2 inhibitor designed to occupy the p53-binding pocket of MDM2. In cancer cells expressing wild-type p53, RG7112 stabilizes p53 and activates the p53 pathway, leading to cell cycle arrest, apoptosis, and inhibition or regression of human tumor xenografts.


    Related Citations: 
    • In vivo activation of the p53 pathway by small-molecule antagonists of MDM2.
      Vassilev, L.T.,Vu, B.T.,Graves, B.,Carvajal, D.,Podlaski, F.,Filipovic, Z.,Kong, N.,Kammlott, U.,Lukacs, C.,Klein, C.,Fotouhi, N.,Liu, E.A.
      (2004) Science 303: 844
    • MDM2 Small-Molecule Antagonist RG7112 Activates p53 Signaling and Regresses Human Tumors in Preclinical Cancer Models.
      Tovar, C.,Graves, B.,Packman, K.,Filipovic, Z.,Xia, B.H.,Tardell, C.,Garrido, R.,Lee, E.,Kolinsky, K.,To, K.H.,Linn, M.,Podlaski, F.,Wovkulich, P.,Vu, B.,Vassilev, L.T.
      (2013) Cancer Res. 73: 2587


    Organizational Affiliation

    Discovery Chemistry, Discovery Oncology, Discovery Technologies, Non-Clinical Development, Roche Research Center, Hoffmann-La Roche, Inc. , 340 Kingsland Street, Nutley, New Jersey 07110, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A
86Xenopus laevisGene Names: mdm2
EC: 6.3.2.-
Find proteins for P56273 (Xenopus laevis)
Go to UniProtKB:  P56273
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NUT
Query on NUT

Download SDF File 
Download CCD File 
A
4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
Nutlin 3a
C30 H30 Cl2 N4 O4
BDUHCSBCVGXTJM-WUFINQPMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NUTIC50: 88 nM BINDINGMOAD
NUTIC50: 88 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 42.887α = 90.00
b = 67.657β = 90.00
c = 67.173γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
CNXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references