4WT2

Co-crystal Structure of MDM2 in Complex with AM-7209


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of AM-7209, a Potent and Selective 4-Amidobenzoic Acid Inhibitor of the MDM2-p53 Interaction.

Rew, Y.Sun, D.Yan, X.Beck, H.P.Canon, J.Chen, A.Duquette, J.Eksterowicz, J.Fox, B.M.Fu, J.Gonzalez, A.Z.Houze, J.Huang, X.Jiang, M.Jin, L.Li, Y.Li, Z.Ling, Y.Lo, M.C.Long, A.M.McGee, L.R.McIntosh, J.Oliner, J.D.Osgood, T.Saiki, A.Y.Shaffer, P.Wang, Y.C.Wortman, S.Yakowec, P.Ye, Q.Yu, D.Zhao, X.Zhou, J.Medina, J.C.Olson, S.H.

(2014) J.Med.Chem. 57: 10499-10511

  • DOI: 10.1021/jm501550p

  • PubMed Abstract: 
  • Structure-based rational design and extensive structure-activity relationship studies led to the discovery of AMG 232 (1), a potent piperidinone inhibitor of the MDM2-p53 association, which is currently being evaluated in human clinical trials for th ...

    Structure-based rational design and extensive structure-activity relationship studies led to the discovery of AMG 232 (1), a potent piperidinone inhibitor of the MDM2-p53 association, which is currently being evaluated in human clinical trials for the treatment of cancer. Further modifications of 1, including replacing the carboxylic acid with a 4-amidobenzoic acid, afforded AM-7209 (25), featuring improved potency (KD from ITC competition was 38 pM, SJSA-1 EdU IC50 = 1.6 nM), remarkable pharmacokinetic properties, and in vivo antitumor activity in both the SJSA-1 osteosarcoma xenograft model (ED50 = 2.6 mg/kg QD) and the HCT-116 colorectal carcinoma xenograft model (ED50 = 10 mg/kg QD). In addition, 25 possesses distinct mechanisms of elimination compared to 1.


    Organizational Affiliation

    Department of Therapeutic Discovery, ‡Department of Pharmaceutics, and §Department of Pharmacokinetics and Drug Metabolism, Amgen Inc. , 1120 Veterans Boulevard, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A
105Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3UD
Query on 3UD

Download SDF File 
Download CCD File 
A
4-({[(3R,5R,6S)-1-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(4-chloro-3-fluorophenyl)-5-(3-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetyl}amino)-2-methoxybenzoic acid
C37 H41 Cl2 F N2 O7 S
QGOICCMBEDDFCI-NXQGQTBASA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3UDIC50: 0.6 nM (100) BINDINGDB
3UDKd: 257 nM (100) BINDINGDB
3UDKd: 0.039 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.176 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 45.517α = 90.00
b = 45.517β = 90.00
c = 208.624γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy