8D4Z | pdb_00008d4z

Crystal structure of USP7 in complex with allosteric inhibitor FX1-3763

• PDB DOI: https://doi.org/10.2210/pdb8D4Z/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-03 Released: 2023-09-20 
• Deposition Author(s): Bell, J.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.190 (DCC) 

Literature

Novel USP7 inhibitors demonstrate potent anti-cancer activity in models of AML, synergy with BCL2 inhibition, and a differentiated mechanism of action

Futran, A.S., Lu, T., Amberg-Johnson, K., Xu, J., Yang, X., He, S., Boyce, S., Bell, J., Pelletier, R., Suzuki, T., Huang, X., Qian, H., Fang, L., Xing, L., Xu, Z., Kurtz, S.E., Tyner, J.W., Tang, W., Guo, T., Akinsanya, K., Madge, D., Jensen, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 85.13 kDa 
• Atom Count: 5,593 
• Modeled Residue Count: 668 
• Deposited Residue Count: 722 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	A, B	361	Homo sapiens	Mutation(s): 0  Gene Names: USP7, HAUSP 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QBL (Subject of Investigation/LOI)	C [auth A], E [auth B]	1-({(7M)-7-[1-(azetidin-3-yl)-6-chloro-1,2,3,4-tetrahydroquinolin-8-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione C24 H23 Cl N4 O2 S JLINGJINOLLCFE-UHFFFAOYSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.260 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.235	α = 90
b = 65.506	β = 94.7
c = 85.086	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PRIME-X	refinement
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Bell, J.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release