5WHC

USP7 in complex with Cpd2 (4-(3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl)phenol)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.548 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Small-Molecule Inhibitors of Ubiquitin Specific Protease 7 (USP7) Using Integrated NMR and in Silico Techniques.

Di Lello, P.Pastor, R.Murray, J.M.Blake, R.A.Cohen, F.Crawford, T.D.Drobnick, J.Drummond, J.Kategaya, L.Kleinheinz, T.Maurer, T.Rouge, L.Zhao, X.Wertz, I.Ndubaku, C.Tsui, V.

(2017) J. Med. Chem. 60: 10056-10070

  • DOI: 10.1021/acs.jmedchem.7b01293

  • PubMed Abstract: 
  • USP7 is a deubiquitinase implicated in destabilizing the tumor suppressor p53, and for this reason it has gained increasing attention as a potential oncology target for small molecule inhibitors. Herein we describe the biophysical, biochemical, and c ...

    USP7 is a deubiquitinase implicated in destabilizing the tumor suppressor p53, and for this reason it has gained increasing attention as a potential oncology target for small molecule inhibitors. Herein we describe the biophysical, biochemical, and computational approaches that led to the identification of 4-(2-aminopyridin-3-yl)phenol compounds described by Kategaya ( Nature 2017 , 550 , 534 - 538 ) as specific inhibitors of USP7. Fragment based lead discovery (FBLD) by NMR combined with virtual screening and re-mining of biochemical high-throughput screening (HTS) hits led to the discovery of a series of ligands that bind in the "palm" region of the catalytic domain of USP7 and inhibit its catalytic activity. These ligands were then optimized by structure-based design to yield cell-active molecules with reasonable physical properties. This discovery process not only involved multiple techniques working in concert but also illustrated a unique way in which hits from orthogonal screening approaches complemented each other for lead identification.


    Organizational Affiliation

    Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, B
346Homo sapiensMutation(s): 0 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
AJJ
Query on AJJ

Download SDF File 
Download CCD File 
A, B
4-[3-(1-methylpiperidin-4-yl)-1,2,4-oxadiazol-5-yl]phenol
C14 H17 N3 O2
BGJREFNVLIBEOU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.548 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.292α = 90.00
b = 69.279β = 95.00
c = 77.070γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references