5HMI | pdb_00005hmi

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 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5HMI

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acsmedchemlett.5b00472
  • Primary Citation Related Structures: 
    5HMH, 5HMI, 5HMK

  • 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-(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.

Macromolecule Content 

  • Total Structure Weight: 25.53 kDa 
  • Atom Count: 1,789 
  • Modeled Residue Count: 196 
  • Deposited Residue Count: 208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B
104Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000135679 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
62T

Query on 62T



Download:Ideal Coordinates CCD File
C [auth A],
E [auth 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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.229 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.473α = 90
b = 38.915β = 90
c = 132.505γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references