4OBA

Co-crystal structure of MDM2 with Inhibitor Compound 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Selective and Potent Morpholinone Inhibitors of the MDM2-p53 Protein-Protein Interaction.

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

(2014) J Med Chem 57: 2472-2488

  • DOI: 10.1021/jm401767k
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We previously reported the discovery of AMG 232, a highly potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Our continued search for potent and diverse analogues led to the discovery of novel morpholinone MDM2 inhibitors. This ...

    We previously reported the discovery of AMG 232, a highly potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Our continued search for potent and diverse analogues led to the discovery of novel morpholinone MDM2 inhibitors. This change to a morpholinone core has a significant impact on both potency and metabolic stability compared to the piperidinone series. Within this morpholinone series, AM-8735 emerged as an inhibitor with remarkable biochemical potency (HTRF IC50 = 0.4 nM) and cellular potency (SJSA-1 EdU IC50 = 25 nM), as well as pharmacokinetic properties. Compound 4 also shows excellent antitumor activity in the SJSA-1 osteosarcoma xenograft model with an ED50 of 41 mg/kg. Lead optimization toward the discovery of this inhibitor as well as key differences between the morpholinone and the piperidinone series will be described herein.


    Organizational Affiliation

    Departments of †Therapeutic Discovery, ‡Pharmaceutics, and §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, B, C
96Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2TW
Query on 2TW

Download CCD File 
A, B, C
[(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid
C27 H31 Cl2 N O6 S
ZTMSSDQFJNEUNG-WMMXXEOUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2TWIC50:  0.4000000059604645   nM  BindingDB
2TWIC50:  1.7999999523162842   nM  BindingDB
2TWIC50:  0.4000000059604645   nM  Binding MOAD
2TWIC50:  160   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.290 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.729α = 90
b = 98.674β = 90
c = 106.687γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references