5NGF

Crystal structure of USP7 in complex with the covalent inhibitor, FT827


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of USP7 inhibition by selective small-molecule inhibitors.

Turnbull, A.P.Ioannidis, S.Krajewski, W.W.Pinto-Fernandez, A.Heride, C.Martin, A.C.L.Tonkin, L.M.Townsend, E.C.Buker, S.M.Lancia, D.R.Caravella, J.A.Toms, A.V.Charlton, T.M.Lahdenranta, J.Wilker, E.Follows, B.C.Evans, N.J.Stead, L.Alli, C.Zarayskiy, V.V.Talbot, A.C.Buckmelter, A.J.Wang, M.McKinnon, C.L.Saab, F.McGouran, J.F.Century, H.Gersch, M.Pittman, M.S.Marshall, C.G.Raynham, T.M.Simcox, M.Stewart, L.M.D.McLoughlin, S.B.Escobedo, J.A.Bair, K.W.Dinsmore, C.J.Hammonds, T.R.Kim, S.Urbe, S.Clague, M.J.Kessler, B.M.Komander, D.

(2017) Nature 550: 481-486

  • DOI: 10.1038/nature24451
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins ...

    Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins, potentially including otherwise 'undruggable' targets. For example, the inhibition of ubiquitin-specific protease 7 (USP7) results in the degradation of the oncogenic E3 ligase MDM2, and leads to re-activation of the tumour suppressor p53 in various cancers. Here we report that two compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Co-crystal structures reveal that both compounds target a dynamic pocket near the catalytic centre of the auto-inhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53, and results in the transcription of p53 target genes, induction of the tumour suppressor p21, and inhibition of tumour growth in mice.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, B
355Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to UniProtKB:  Q93009
NIH Common Fund Data Resources
PHAROS  Q93009
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8WN
Query on 8WN

Download CCD File 
A, B
~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide
C27 H30 N6 O5 S
RLNXXNBZMTXHGJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.81α = 105.05
b = 63.31β = 107.88
c = 65.66γ = 113.03
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Structure summary
  • Version 1.2: 2017-11-01
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Database references