5VS6

Structure of DUB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7.

Lamberto, I.Liu, X.Seo, H.S.Schauer, N.J.Iacob, R.E.Hu, W.Das, D.Mikhailova, T.Weisberg, E.L.Engen, J.R.Anderson, K.C.Chauhan, D.Dhe-Paganon, S.Buhrlage, S.J.

(2017) Cell Chem Biol 24: 1490-1500.e11

  • DOI: 10.1016/j.chembiol.2017.09.003
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially protei ...

    Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.


    Organizational Affiliation

    Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: saraj_buhrlage@dfci.harvard.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, B
353Homo 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9QD
Query on 9QD

Download CCD File 
A, B
N-[3-({4-hydroxy-1-[(3R)-3-phenylbutanoyl]piperidin-4-yl}methyl)-4-oxo-3,4-dihydroquinazolin-7-yl]-3-(4-methylpiperazin-1-yl)propanamide
C32 H42 N6 O4
QLBYDWATOPNXBG-XMMPIXPASA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9QDIC50:  193   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.8α = 90
b = 68.52β = 96.17
c = 80.31γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references