6F5H

Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Identification and Structure-Guided Development of Pyrimidinone Based USP7 Inhibitors.

O'Dowd, C.R.Helm, M.D.Rountree, J.S.S.Flasz, J.T.Arkoudis, E.Miel, H.Hewitt, P.R.Jordan, L.Barker, O.Hughes, C.Rozycka, E.Cassidy, E.McClelland, K.Odrzywol, E.Page, N.Feutren-Burton, S.Dvorkin, S.Gavory, G.Harrison, T.

(2018) ACS Med Chem Lett 9: 238-243

  • DOI: 10.1021/acsmedchemlett.7b00512
  • Primary Citation of Related Structures:  
    6F5H

  • PubMed Abstract: 
  • Ubiquitin specific protease 7 (USP7, HAUSP) has become an attractive target in drug discovery due to the role it plays in modulating Mdm2 levels and consequently p53. Increasing interest in USP7 is emerging due to its potential involvement in oncogenic pathways as well as possible roles in both metabolic and immune disorders in addition to viral infections ...

    Ubiquitin specific protease 7 (USP7, HAUSP) has become an attractive target in drug discovery due to the role it plays in modulating Mdm2 levels and consequently p53. Increasing interest in USP7 is emerging due to its potential involvement in oncogenic pathways as well as possible roles in both metabolic and immune disorders in addition to viral infections. Potent, novel, and selective inhibitors of USP7 have been developed using both rational and structure-guided design enabled by high-resolution cocrystallography. Initial hits were identified via fragment-based screening, scaffold-hopping, and hybridization exercises. Two distinct subseries are described along with associated structure-activity relationship trends, as are initial efforts aimed at developing compounds suitable for in vivo experiments. Overall, these discoveries will enable further research into the wider biological role of USP7.


    Organizational Affiliation

    Centre for Cancer Research and Cell Biology, Queen's University Belfast, Northern Ireland BT9 7AE, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7A, B357Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CQ5 (Subject of Investigation/LOI)
Query on CQ5

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]-6-(2-pyrrolidin-1-ylethylamino)pyrimidin-4-one
C26 H37 N5 O3
VJDZJAUBPMXVAF-OAQYLSRUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], F [auth B], G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CQ5 Binding MOAD:  6F5H IC50: 87 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.865α = 90
b = 67.328β = 105.06
c = 80.686γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release