1RV1

CRYSTAL STRUCTURE OF HUMAN MDM2 WITH AN IMIDAZOLINE INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1RV1/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2003-12-12 Released: 2004-01-20 
• Deposition Author(s): Lukacs, C., Kammlott, U., Graves, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.322 
• R-Value Work: 0.256 
• R-Value Observed: 0.266 

Starting Model: experimental

Literature

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: 844-848

• PubMed: 14704432 
• DOI: https://doi.org/10.1126/science.1092472
• Primary Citation of Related Structures:  
  1RV1


• PubMed Abstract: 
  

  MDM2 binds the p53 tumor suppressor protein with high affinity and negatively modulates its transcriptional activity and stability. Overexpression of MDM2, found in many human tumors, effectively impairs p53 function. Inhibition of MDM2-p53 interaction can stabilize p53 and may offer a novel strategy for cancer therapy. Here, we identify potent and selective small-molecule antagonists of MDM2 and confirm their mode of action through the crystal structures of complexes. These compounds bind MDM2 in the p53-binding pocket and activate the p53 pathway in cancer cells, leading to cell cycle arrest, apoptosis, and growth inhibition of human tumor xenografts in nude mice.

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Organizational Affiliation: 

Department of Discovery Oncology, Roche Research Center, Hoffmann-La Roche, Inc., Nutley, NJ 07110, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.61 kDa 
• Atom Count: 2,357 
• Modelled Residue Count: 255 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-protein ligase E3 Mdm2	A, B, C	85	Homo sapiens	Mutation(s): 1  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMZ	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C]	CIS-[4,5-BIS-(4-BROMOPHENYL)-2-(2-ETHOXY-4-METHOXYPHENYL)-4,5-DIHYDROIMIDAZOL-1-YL]-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]METHANONE C31 H34 Br2 N4 O4 PVRYEWOXWGDQHA-URLMMPGGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IMZ	BindingDB:  1RV1	IC50: min: 100, max: 140 (nM) from 2 assay(s)
	PDBBind:  1RV1	IC50: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.322 
• R-Value Work: 0.256 
• R-Value Observed: 0.266 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.264	α = 90
b = 39.727	β = 114.29
c = 79.362	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-20 
Deposition Author(s): Lukacs, C., Kammlott, U., Graves, B.

Revision History  

• Version 1.0: 2004-01-20
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description