› 5whc

X-ray diffraction
2.55Å resolution

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

Released:
DOI: 10.2210/pdb5whc/pdb
PDB entry 5whc coloured by chain, front view.
PDB entry 5whc coloured by chain, side view.
PDB entry 5whc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Small-Molecule Inhibitors of Ubiquitin Specific Protease 7 (USP7) Using Integrated NMR and in Silico Techniques.
Di Lello P, Pastor R, Murray JM, Blake RA, Cohen F, Crawford TD, Drobnick J, Drummond J, Kategaya L, Kleinheinz T, Maurer T, Rougé L, Zhao X, Wertz I, Ndubaku C, Tsui V
J Med Chem 60 10056-10070 (2017)
PMID: 29166018

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187973 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 7 Chains: A, B
Molecule details ›
Chains: A, B
Length: 346 amino acids
Theoretical weight: 40.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q93009 (Residues: 209-554; Coverage: 31%)
Gene names: HAUSP, USP7
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: ubp-family deubiquitinating enzyme superfamily

Ligands and Environments

2 bound ligands:
Ligand AJJ 2 x AJJ
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P21
Unit cell:
a: 76.292Å b: 69.279Å c: 77.07Å
α: 90° β: 95° γ: 90°
R-values:
R R work R free
0.211 0.209 0.26
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

USP7: Structure, substrate specificity, and inhibition.
Pozhidaeva et al. (2019)
14 more

3 mentions without citation

Advances in the Development Ubiquitin-Specific Peptidase (USP) Inhibitors.
Chen et al. (2021)
2 more