4ODF

Co-Crystal Structure of MDM2 with Inhibitor Compound 47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Novel Inhibitors of the MDM2-p53 Interaction Featuring Hydrogen Bond Acceptors as Carboxylic Acid Isosteres.

Gonzalez, A.Z.Li, Z.Beck, H.P.Canon, J.Chen, A.Chow, D.Duquette, J.Eksterowicz, J.Fox, B.M.Fu, J.Huang, X.Houze, J.Jin, L.Li, Y.Ling, Y.Lo, M.C.Long, A.M.McGee, L.R.McIntosh, J.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.Sun, D.Medina, J.C.

(2014) J Med Chem 57: 2963-2988

  • DOI: 10.1021/jm401911v
  • Primary Citation of Related Structures:  
    4OCC, 4ODE, 4ODF, 4OGT, 4OGV, 4OGN

  • PubMed Abstract: 
  • We previously reported the discovery of potent and selective morpholinone and piperidinone inhibitors of the MDM2-p53 interaction. These inhibitors have in common a carboxylic acid moiety that engages in an electrostatic interaction with MDM2-His96. ...

    We previously reported the discovery of potent and selective morpholinone and piperidinone inhibitors of the MDM2-p53 interaction. These inhibitors have in common a carboxylic acid moiety that engages in an electrostatic interaction with MDM2-His96. Our continued search for potent and diverse inhibitors led to the discovery of novel replacements for these acids uncovering new interactions with the MDM2 protein. In particular, using pyridine or thiazole as isosteres of the carboxylic acid moiety resulted in very potent analogues. From these, AM-6761 (4) emerged as a potent inhibitor with remarkable biochemical (HTRF IC50 = 0.1 nM) and cellular potency (SJSA-1 EdU IC50 = 16 nM), as well as favorable pharmacokinetic properties. Compound 4 also shows excellent antitumor activity in the SJSA-1 osteosarcoma xenograft model with an ED50 of 11 mg/kg. Optimization efforts toward the discovery of these inhibitors as well as the new interactions observed with the MDM2 protein are 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A105Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2U1
Query on 2U1

Download Ideal Coordinates CCD File 
A
6-{[(2S,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-2-methyl-3-oxomorpholin-2-yl]methyl}pyridine-3-carboxylic acid
C33 H36 Cl2 N2 O6 S
OTQRFDJHHZHHNT-LNHQPZRBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2U1IC50:  0.10000000149011612   nM  Binding MOAD
2U1IC50:  0.10000000149011612   nM  BindingDB
2U1IC50:  1   nM  BindingDB
2U1IC50:  0.10000000149011612   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.264 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.211α = 90
b = 44.211β = 90
c = 208.882γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
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: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description