4JSC | pdb_00004jsc

The 2.5A crystal structure of humanized Xenopus MDM2 with RO5316533 - a pyrrolidine MDM2 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4JSC/pdb

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


• Deposited: 2013-03-22 Released: 2013-07-24 
• Deposition Author(s): Janson, C.A., Lukacs, C., Graves, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.370 (Depositor), 0.349 (DCC) 
• R-Value Work: 
  0.312 (Depositor), 0.301 (DCC) 
• R-Value Observed: 
  0.316 (Depositor) 

Literature

Discovery of RG7388, a Potent and Selective p53-MDM2 Inhibitor in Clinical Development.

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

(2013) J Med Chem 56: 5979-5983

• PubMed: 23808545 
• DOI: https://doi.org/10.1021/jm400487c
• Primary Citation Related Structures: 
  4JRG, 4JSC


• PubMed Abstract: 
  

  Restoration of p53 activity by inhibition of the p53-MDM2 interaction has been considered an attractive approach for cancer treatment. However, the hydrophobic protein-protein interaction surface represents a significant challenge for the development of small-molecule inhibitors with desirable pharmacological profiles. RG7112 was the first small-molecule p53-MDM2 inhibitor in clinical development. Here, we report the discovery and characterization of a second generation clinical MDM2 inhibitor, RG7388, with superior potency and selectivity.

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Organizational Affiliation: 
• Discovery Chemistry, ‡Discovery Technologies, §Discovery Oncology, ∥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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.03 kDa 
• Atom Count: 1,474 
• Modeled Residue Count: 166 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1OY	C [auth A], D [auth B]	(3S,4R,5S)-3-(3-chloro-2-fluorophenyl)-4-(4-chloro-2-fluorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide C27 H31 Cl2 F2 N3 O3 MSOWFEGZEMCNQZ-UIHIWPSYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.370 (Depositor), 0.349 (DCC) 
• R-Value Work:  0.312 (Depositor), 0.301 (DCC) 
• R-Value Observed: 0.316 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.49	α = 90
b = 73.72	β = 108.44
c = 40.968	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
CNX	refinement
CrystalClear	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Janson, C.A., Lukacs, C., Graves, B.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations