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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.260 (Depositor), 0.254 (DCC)
R-Value Work:
0.203 (Depositor), 0.197 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QBL (Subject of Investigation/LOI) Query on QBL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.260 (Depositor), 0.254 (DCC)
R-Value Work: 0.203 (Depositor), 0.197 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.