7NUS | pdb_00007nus

X-RAY STRUCTURE OF HDM2/CMR19 AT 1.45A: Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors

• PDB DOI: https://doi.org/10.2210/pdb7NUS/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-13 Released: 2021-09-22 
• Deposition Author(s): Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors.

Schneider, A.F.L., Kallen, J., Ottl, J., Reid, P.C., Ripoche, S., Ruetz, S., Stachyra, T.M., Hintermann, S., Dumelin, C.E., Hackenberger, C.P.R., Marzinzik, A.L.

(2021) RSC Chem Biol 2: 1661-1668

• PubMed: 34977581 
• DOI: https://doi.org/10.1039/d1cb00056j
• Primary Citation Related Structures: 
  7NUS


• PubMed Abstract: 
  

  Mouse double minute 2 homolog (MDM2, Hdm2) is an important negative regulator of the tumor suppressor p53. Using a mRNA based display technique to screen a library of >10 ¹² in vitro -translated cyclic peptides, we have identified a macrocyclic ligand that shows picomolar potency on MDM2. X-Ray crystallography reveals a novel binding mode utilizing a unique pharmacophore to occupy the Phe/Trp/Leu pockets on MDM2. Conjugation of a cyclic cell-penetrating peptide (cCPP) to the initially non cell-permeable ligand enables cellular uptake and a pharmacodynamic response in SJSA-1 cells. The demonstrated enhanced intracellular availability of cyclic peptides that are identified by a display technology exemplifies a process for the application of intracellular tools for drug discovery projects.

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Organizational Affiliation: 
• Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10 Berlin 13125 Germany [e-mail].
Novartis Institutes for BioMedical Research, Novartis Campus Basel CH-4056 Switzerland [e-mail].
PeptiDream, 3-25-23 Tonomachi Kawasaki-Ku Kanagawa 210-0821 Japan.
Humboldt Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2 Berlin 12489 Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.4 kDa 
• Atom Count: 3,159 
• Modeled Residue Count: 314 
• Deposited Residue Count: 333 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B, C	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p53/MDM2 macrocyclic peptide inhibitor	D, E, F	15	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	I [auth E], J [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BIF	D, E, F	L-PEPTIDE LINKING	C15 H15 N O2		PHE
CCS	D, E, F	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.78	α = 90
b = 40.306	β = 112.2
c = 70.198	γ = 90

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

• Released Date: 2021-09-22 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2021-09-29
  Changes: Derived calculations
• Version 1.2: 2022-02-02
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description