4OAS

co-crystal structure of MDM2 (17-111) in complex with compound 25

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of AMG 232, a Potent, Selective, and Orally Bioavailable MDM2-p53 Inhibitor in Clinical Development.

Sun, D., Li, Z., Rew, Y., Gribble, M., Bartberger, M.D., Beck, H.P., Canon, J., Chen, A., Chen, X., Chow, D., Deignan, J., Duquette, J., Eksterowicz, J., Fisher, B., Fox, B.M., Fu, J., Gonzalez, A.Z., Gonzalez-Lopez De Turiso, F., Houze, J.B., Huang, X., Jiang, M., Jin, L., Kayser, F., Liu, J.J., Lo, M.C., Long, A.M., Lucas, B., McGee, L.R., McIntosh, J., Mihalic, J., Oliner, J.D., Osgood, T., Peterson, M.L., Roveto, P., Saiki, A.Y., Shaffer, P., Toteva, M., Wang, Y., Wang, Y.C., Wortman, S., Yakowec, P., Yan, X., Ye, Q., Yu, D., Yu, M., Zhao, X., Zhou, J., Zhu, J., Olson, S.H., Medina, J.C.

(2014) J Med Chem 57: 1454-1472

  • DOI: 10.1021/jm401753e
  • Primary Citation of Related Structures:  
    4OAS

  • PubMed Abstract: 

    • We recently reported the discovery of AM-8553 (1), a potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Continued research investigation of the N-alkyl substituent of this series, focused in particular on a previously underutilized interaction in a shallow cleft on the MDM2 surface, led to the discovery of a one-carbon tethered sulfone which gave rise to substantial improvements in biochemical and cellular potency ...

    We recently reported the discovery of AM-8553 (1), a potent and selective piperidinone inhibitor of the MDM2-p53 interaction. Continued research investigation of the N-alkyl substituent of this series, focused in particular on a previously underutilized interaction in a shallow cleft on the MDM2 surface, led to the discovery of a one-carbon tethered sulfone which gave rise to substantial improvements in biochemical and cellular potency. Further investigation produced AMG 232 (2), which is currently being evaluated in human clinical trials for the treatment of cancer. Compound 2 is an extremely potent MDM2 inhibitor (SPR KD = 0.045 nM, SJSA-1 EdU IC50 = 9.1 nM), with remarkable pharmacokinetic properties and in vivo antitumor activity in the SJSA-1 osteosarcoma xenograft model (ED50 = 9.1 mg/kg).

    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 Mdm2A, C, E96Homo 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
GTEx  ENSG00000135679
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SW
Query on 2SW
Download Ideal Coordinates CCD File 
A, C, E
[(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid
C28 H35 Cl2 N O5 S
AXQMSOFCQLTJGV-ZJTSJXPUSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2SWKd:  0.03999999910593033   nM  BindingDB
2SWIC50:  1.100000023841858   nM  BindingDB
2SWIC50:  0.10000000149011612   nM  BindingDB
2SWIC50:  18   nM  BindingDB
2SWKd:  0.04500000178813934   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.554α = 90
b = 99.035β = 90
c = 107.076γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-01-06 
  • Released Date: 2014-02-19 
    • Deposition Author(s): Huang, X.

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references