4J3E | pdb_00004j3e

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

• PDB DOI: https://doi.org/10.2210/pdb4J3E/pdb

• Classification: LIGASE/ANTAGONIST
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-02-05 Released: 2013-04-24 
• Deposition Author(s): Graves, B.J., Lukacs, C.M., Kammlott, R.U., Crowther, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.239 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

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

• PubMed: 24900694 
• DOI: https://doi.org/10.1021/ml4000657
• Primary Citation Related Structures: 
  4J3E


• 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. 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.64 kDa 
• Atom Count: 877 
• Modeled Residue Count: 86 
• Deposited Residue Count: 86 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	86	Xenopus laevis	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUT	B [auth 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 C30 H30 Cl2 N4 O4 BDUHCSBCVGXTJM-WUFINQPMSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.239 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.887	α = 90
b = 67.657	β = 90
c = 67.173	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Graves, B.J., Lukacs, C.M., Kammlott, R.U., Crowther, R.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2014-10-08
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations