Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 11.90 kDa 
• Atom Count: 873 
• Modelled Residue Count: 97 
• Deposited Residue Count: 97 
• Unique protein chains: 1

5OAI

Structure of MDM2 with low molecular weight inhibitor

• PDB DOI: 10.2210/pdb5OAI/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-22 Released: 2019-02-13 
• Deposition Author(s): Twarda-Clapa, A., Neochoritis, C.G., Grudnik, P., Dubin, G., Domling, A., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

A fluorinated indole-based MDM2 antagonist selectively inhibits the growth of p53wtosteosarcoma cells.

Skalniak, L., Twarda-Clapa, A., Neochoritis, C.G., Surmiak, E., Machula, M., Wisniewska, A., Labuzek, B., Ali, A.M., Krzanik, S., Dubin, G., Groves, M., Domling, A., Holak, T.A.

(2019) FEBS J 286: 1360-1374

• PubMed: 30715803 
• DOI: 10.1111/febs.14774
• Primary Citation of Related Structures:  
  5OAI


• PubMed Abstract: 
  

The p53 protein is engaged in the repair of DNA mutations and elimination of heavily damaged cells, providing anticancer protection. Dysregulation of p53 activity is a crucial step in carcinogenesis. This dysregulation is often caused by the overexpression of negative regulators of p53, among which MDM2 is the most prominent one. Antagonizing MDM2 with small molecules restores the activity of p53 in p53 wild-type (p53 ^wt ) cells and thus provides positive outcomes in the treatment of p53 ^wt cancers. Previously, we have reported the discovery of a panel of fluoro-substituted indole-based antagonists of MDM2. Here, we demonstrate the biological activity and stereoselectivity of the most active compound from this series. Both enantiomers of the esterified form of the compound, as well as its corresponding carboxylic acids, were found active in fluorescence polarization (FP) assay, nuclear magnetic resonance (NMR) and microscale thermophoresis (MST) assay, with K _i and K _D values around 1 μm. From these four compounds, the esterified enantiomer (R)-5a was active in cells, which was evidenced by the increase of p53 levels, the induced expression of p53-target genes (CDKN1A and MDM2), the selective induction of cell cycle arrest, and selective growth inhibition of p53 ^wt U-2 OS and SJSA-1 compared to p53 ^del SAOS-2 cells. The analysis of the crystal structure of human MDM2 in complex with the compound (R)-6a (carboxylic acid of the active (R)-5a compound) revealed the classical three-finger binding mode. Altogether, our data demonstrate the activity of the compound and provide the structural basis for further structure optimization.

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Organizational Affiliation: 

Faculty of Chemistry, Jagiellonian University, Krakow, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	97	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B5K	B [auth A]	3-[(1~{R})-2-(~{tert}-butylamino)-1-[methanoyl-[[3,4,5-tris(fluoranyl)phenyl]methyl]amino]-2-oxidanylidene-ethyl]-6-chloranyl-1~{H}-indole-2-carboxylic acid C23 H21 Cl F3 N3 O4 FZINKXKQKUDBDP-HXUWFJFHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B5K	Binding MOAD:  5OAI	Ki: 100 (nM) from 1 assay(s)
	BindingDB:  5OAI	Ki: min: 0.13, max: 130 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.227 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.731	α = 90
b = 59.216	β = 90
c = 83.897	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-06-22 
• Released Date: 2019-02-13 
Deposition Author(s): Twarda-Clapa, A., Neochoritis, C.G., Grudnik, P., Dubin, G., Domling, A., Holak, T.A.

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references