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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 11.88 kDa 
• Atom Count: 961 
• Modelled Residue Count: 95 
• Deposited Residue Count: 96 
• Unique protein chains: 1

5LN2

Discovery of a novel class of highly potent inhibitors of the p53-MDM2 interaction by structure-based design starting from a conformational argument

• PDB DOI: 10.2210/pdb5LN2/pdb

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


• Deposited: 2016-08-02 Released: 2016-09-07 
• Deposition Author(s): Kallen, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Discovery of a novel class of highly potent inhibitors of the p53-MDM2 interaction by structure-based design starting from a conformational argument.

Furet, P., Masuya, K., Kallen, J., Stachyra-Valat, T., Ruetz, S., Guagnano, V., Holzer, P., Mah, R., Stutz, S., Vaupel, A., Chene, P., Jeay, S., Schlapbach, A.

(2016) Bioorg Med Chem Lett 26: 4837-4841

• PubMed: 27542305 
• DOI: 10.1016/j.bmcl.2016.08.010
• Primary Citation of Related Structures:  
  5LN2


• PubMed Abstract: 
  

The p53-MDM2 interaction is an anticancer drug target under investigation in the clinic. Our compound NVP-CGM097 is one of the small molecule inhibitors of this protein-protein interaction currently evaluated in cancer patients. As part of our effort to identify new classes of p53-MDM2 inhibitors that could lead to additional clinical candidates, we report here the design of highly potent inhibitors having a pyrazolopyrrolidinone core structure. The conception of these new inhibitors originated in a consideration on the MDM2 bound conformation of the dihydroisoquinolinone class of inhibitors to which NVP-CGM097 belongs. This work forms the foundation of the discovery of HDM201, a second generation p53-MDM2 inhibitor that recently entered phase I clinical trial.

---

Organizational Affiliation: 

Novartis Institutes for BioMedical Research, WKL-136.P.12, CH-4002 Basel, Switzerland.

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: 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZT	B [auth A]	(4~{S})-5-[5-chloranyl-2-[2-(dimethylamino)ethoxy]phenyl]-4-(4-chloranyl-2-methyl-phenyl)-2-(2-methoxyphenyl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one C32 H34 Cl2 N4 O3 YBMQYNARIZUNIO-HKBQPEDESA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
6ZT	BindingDB:  5LN2	IC50: min: 0.1, max: 1.7 (nM) from 3 assay(s)
	Binding MOAD:  5LN2	IC50: 0.13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.247 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.54	α = 90
b = 56.54	β = 90
c = 103.953	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-02 
• Released Date: 2016-09-07 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Database references