5UQV

USP7 in complex with GNE6640 (4-(2-amino-4-ethyl-5-(1H-indazol-5-yl)pyridin-3-yl)phenol)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

USP7 small-molecule inhibitors interfere with ubiquitin binding.

Kategaya, L.Di Lello, P.Rouge, L.Pastor, R.Clark, K.R.Drummond, J.Kleinheinz, T.Lin, E.Upton, J.P.Prakash, S.Heideker, J.McCleland, M.Ritorto, M.S.Alessi, D.R.Trost, M.Bainbridge, T.W.Kwok, M.C.M.Ma, T.P.Stiffler, Z.Brasher, B.Tang, Y.Jaishankar, P.Hearn, B.R.Renslo, A.R.Arkin, M.R.Cohen, F.Yu, K.Peale, F.Gnad, F.Chang, M.T.Klijn, C.Blackwood, E.Martin, S.E.Forrest, W.F.Ernst, J.A.Ndubaku, C.Wang, X.Beresini, M.H.Tsui, V.Schwerdtfeger, C.Blake, R.A.Murray, J.Maurer, T.Wertz, I.E.

(2017) Nature 550: 534-538

  • DOI: https://doi.org/10.1038/nature24006
  • Primary Citation of Related Structures:  
    5UQV, 5UQX

  • PubMed Abstract: 

    The ubiquitin system regulates essential cellular processes in eukaryotes. Ubiquitin is ligated to substrate proteins as monomers or chains and the topology of ubiquitin modifications regulates substrate interactions with specific proteins. Thus ubiquitination directs a variety of substrate fates including proteasomal degradation. Deubiquitinase enzymes cleave ubiquitin from substrates and are implicated in disease; for example, ubiquitin-specific protease-7 (USP7) regulates stability of the p53 tumour suppressor and other proteins critical for tumour cell survival. However, developing selective deubiquitinase inhibitors has been challenging and no co-crystal structures have been solved with small-molecule inhibitors. Here, using nuclear magnetic resonance-based screening and structure-based design, we describe the development of selective USP7 inhibitors GNE-6640 and GNE-6776. These compounds induce tumour cell death and enhance cytotoxicity with chemotherapeutic agents and targeted compounds, including PIM kinase inhibitors. Structural studies reveal that GNE-6640 and GNE-6776 non-covalently target USP7 12 Å distant from the catalytic cysteine. The compounds attenuate ubiquitin binding and thus inhibit USP7 deubiquitinase activity. GNE-6640 and GNE-6776 interact with acidic residues that mediate hydrogen-bond interactions with the ubiquitin Lys48 side chain, suggesting that USP7 preferentially interacts with and cleaves ubiquitin moieties that have free Lys48 side chains. We investigated this idea by engineering di-ubiquitin chains containing differential proximal and distal isotopic labels and measuring USP7 binding by nuclear magnetic resonance. This preferential binding protracted the depolymerization kinetics of Lys48-linked ubiquitin chains relative to Lys63-linked chains. In summary, engineering compounds that inhibit USP7 activity by attenuating ubiquitin binding suggests opportunities for developing other deubiquitinase inhibitors and may be a strategy more broadly applicable to inhibiting proteins that require ubiquitin binding for full functional activity.


  • Organizational Affiliation

    Department of Discovery Oncology, Genentech, South San Francisco, California 94080, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7
A, B
368Homo 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
GTEx:  ENSG00000187555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
8JM BindingDB:  5UQV IC50: min: 750, max: 2100 (nM) from 3 assay(s)
EC50: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.788α = 90
b = 68.435β = 95.45
c = 76.739γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description