8PWC | pdb_00008pwc

Crystal structure of MDM2 with Brigimadlin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.226 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery and Characterization of Brigimadlin, a Novel and Highly Potent MDM2-p53 Antagonist Suitable for Intermittent Dose Schedules.

Gollner, A.Rudolph, D.Weyer-Czernilofsky, U.Baumgartinger, R.Jung, P.Weinstabl, H.Ramharter, J.Grempler, R.Quant, J.Rinnenthal, J.Perez Pitarch, A.Golubovic, B.Gerlach, D.Bader, G.Wetzel, K.Otto, S.Mandl, C.Boehmelt, G.McConnell, D.B.Kraut, N.Sini, P.

(2024) Mol Cancer Ther 23: 1689-1702

  • DOI: https://doi.org/10.1158/1535-7163.MCT-23-0783
  • Primary Citation Related Structures: 
    8PWC

  • PubMed Abstract: 

    p53 is known as the guardian of the genome and is one of the most important tumor-suppressors. It is inactivated in most tumors, either via tumor protein p53 (TP53) gene mutation or copy number amplification of key negative regulators, e.g., mouse double minute 2 (MDM2). Compounds that bind to the MDM2 protein and disrupt its interaction with p53 restore p53 tumor suppressor activity, thereby promoting cell cycle arrest and apoptosis. Previous clinical experience with MDM2-p53 protein-protein interaction antagonists (MDM2-p53 antagonists) have demonstrated that thrombocytopenia and neutropenia represent on-target dose-limiting toxicities that might restrict their therapeutic utility. Dosing less frequently, while maintaining efficacious exposure, represents an approach to mitigate toxicity and improve the therapeutic window of MDM2-p53 antagonists. However, to achieve this, a molecule possessing excellent potency and ideal pharmacokinetic properties is required. Here, we present the discovery and characterization of brigimadlin (BI 907828), a novel, investigational spiro-oxindole MDM2-p53 antagonist. Brigimadlin exhibited high bioavailability and exposure, as well as dose-linear pharmacokinetics in preclinical models. Brigimadlin treatment restored p53 activity and led to apoptosis induction in preclinical models of TP53 wild-type, MDM2-amplified cancer. Oral administration of brigimadlin in an intermittent dosing schedule induced potent tumor growth inhibition in several TP53 wild-type, MDM2-amplified xenograft models. Exploratory clinical pharmacokinetic studies (NCT03449381) showed high systemic exposure and a long plasma elimination half-life in cancer patients who received oral brigimadlin. These findings support the continued clinical evaluation of brigimadlin in patients with MDM2-amplified cancers, such as dedifferentiated liposarcoma.


  • Organizational Affiliation
    • Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.

Macromolecule Content 

  • Total Structure Weight: 39.55 kDa 
  • Atom Count: 2,618 
  • Modeled Residue Count: 276 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B, C
110Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.226 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.207α = 90
b = 83.207β = 90
c = 42.056γ = 120
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata reduction
autoPROCdata scaling
Aimlessdata scaling
BUSTERrefinement
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-12-11
    Changes: Database references, Structure summary