4OGV

Co-Crystal Structure of MDM2 with Inhibitor Compound 49

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 

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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, 4OGN, 4OGT, 4OGV

  • 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. 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2A, B, C95Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2U7
Query on 2U7
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		[(2S,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid
C26 H31 Cl2 N O6 S
UQONPZNBMIQADI-NEUULRRLSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
2U7 Binding MOAD:  4OGV IC50: 9 (nM) from 1 assay(s)
BindingDB:  4OGV IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.301α = 90
b = 97.412β = 90
c = 105.129γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references