6GGN

In vitro and in vivo characterization of a novel, highly potent p53-MDM2 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6GGN/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-05-03 Released: 2018-09-26 
• Deposition Author(s): Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

In vitro and in vivo characterization of a novel, highly potent p53-MDM2 inhibitor.

Vaupel, A., Holzer, P., Ferretti, S., Guagnano, V., Kallen, J., Mah, R., Masuya, K., Ruetz, S., Rynn, C., Schlapbach, A., Stachyra, T., Stutz, S., Todorov, M., Jeay, S., Furet, P.

(2018) Bioorg Med Chem Lett 28: 3404-3408

• PubMed: 30217415 
• DOI: https://doi.org/10.1016/j.bmcl.2018.08.027
• Primary Citation of Related Structures:  
  6GGN


• PubMed Abstract: 
  

  Small molecule inhibitors of the p53-MDM2 protein complex are under intense investigation in clinical trials as anti-cancer agents, including our first generation inhibitor NVP-CGM097. We recently described the rational design of a novel pyrazolopyrrolidinone core as a new lead structure and now we report on the synthesis and optimization of this to provide a highly potent lead compound. This new compound displayed excellent oral efficacy in our preclinical mechanistic in vivo model and marked a significant milestone towards the identification of our second generation clinical candidate NVP-HDM201.

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Organizational Affiliation: 

Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. Electronic address: [e-mail].

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: 11.74 kDa 
• Atom Count: 878 
• Modelled Residue Count: 94 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A	96	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 GTEx:  ENSG00000135679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EYH (Subject of Investigation/LOI)	B [auth A]	(4~{S})-4-(4-chloranyl-2-methyl-phenyl)-5-(5-chloranyl-2-methyl-phenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one C28 H27 Cl2 N5 O3 XBJHBEQDHSREQB-QHCPKHFHSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
EYH	BindingDB:  6GGN	IC50: min: 0.07, max: 0.17 (nM) from 4 assay(s)
	Binding MOAD:  6GGN	IC50: 0.08 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.08	α = 90
b = 56.08	β = 90
c = 106.698	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2018-10-24
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description