5HMI

HDM2 in complex with a 3,3-Disubstituted Piperidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Novel 3,3-Disubstituted Piperidines as Orally Bioavailable, Potent, and Efficacious HDM2-p53 Inhibitors.

Bogen, S.L.Pan, W.Gibeau, C.R.Lahue, B.R.Ma, Y.Nair, L.G.Seigel, E.Shipps, G.W.Tian, Y.Wang, Y.Lin, Y.Liu, M.Liu, S.Mirza, A.Wang, X.Lipari, P.Seidel-Dugan, C.Hicklin, D.J.Bishop, W.R.Rindgen, D.Nomeir, A.Prosise, W.Reichert, P.Scapin, G.Strickland, C.Doll, R.J.

(2016) Acs Med.Chem.Lett. 7: 324-329

  • DOI: 10.1021/acsmedchemlett.5b00472
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A new subseries of substituted piperidines as p53-HDM2 inhibitors exemplified by 21 has been developed from the initial lead 1. Research focused on optimization of a crucial HDM2 Trp23-ligand interaction led to the identification of 2-(trifluoromethy ...

    A new subseries of substituted piperidines as p53-HDM2 inhibitors exemplified by 21 has been developed from the initial lead 1. Research focused on optimization of a crucial HDM2 Trp23-ligand interaction led to the identification of 2-(trifluoromethyl)thiophene as the preferred moiety. Further investigation of the Leu26 pocket resulted in potent, novel substituted piperidine inhibitors of the HDM2-p53 interaction that demonstrated tumor regression in several human cancer xenograft models in mice. The structure of HDM2 in complex with inhibitors 3, 10, and 21 is described.


    Organizational Affiliation

    Discovery Chemistry, Merck Research Laboratories , Kenilworth, New Jersey 07033, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
104Homo sapiensMutation(s): 2 
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
62T
Query on 62T

Download SDF File 
Download CCD File 
A, B
{4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]methanone
C33 H36 F6 N4 O5 S
KEKDAGVCTZPOAA-JOMNFKBKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.473α = 90.00
b = 38.915β = 90.00
c = 132.505γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
d*TREKdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-01-16 
  • Released Date: 2016-04-06 
  • Deposition Author(s): Scapin, G.

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Derived calculations, Refinement description