9EBS

Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization of TNG348: a selective, allosteric USP1 inhibitor that synergizes with PARP inhibitors in tumors with homologous recombination deficiency.

Simoneau, A.Pratt, C.B.Wu, H.J.Rajeswaran, S.S.Comer, C.G.Sudsakorn, S.Zhang, W.Liu, S.Meier, S.R.Choi, A.H.Khendu, T.Stowe, H.Shen, B.Whittington, D.A.Chen, Y.Yu, Y.Mallender, W.D.Feng, T.Andersen, J.N.Maxwell, J.P.Throner, S.

(2025) Mol Cancer Ther 

  • DOI: https://doi.org/10.1158/1535-7163.MCT-24-0515
  • Primary Citation of Related Structures:  
    9EBS

  • PubMed Abstract: 

    Inhibition of the deubiquitinating enzyme USP1 can induce synthetic lethality in tumors characterized by homologous recombination deficiency (HRD) and represents a novel therapeutic strategy for the treatment of BRCA1/2 mutant cancers, potentially including patients whose tumors have primary or acquired resistance to PARP inhibitors (PARPi). Here, we present a comprehensive characterization of TNG348, an allosteric, selective, and reversible inhibitor of USP1 (USP1i). TNG348 induces dose-dependent accumulation of ubiquitinated protein substrates both in vitro and in vivo. CRISPR screens show that TNG348 exerts its anti-tumor effect by disrupting the translesion synthesis pathway of DNA damage tolerance through RAD18-dependent ub-PCNA induction. Though TNG348 and PARPi share the ability to selectively kill HRD tumor cells, CRISPR screens reveal that TNG348 and PARPi do so through discrete mechanisms. Particularly, knocking out PARP1 causes resistance to PARPi but sensitizes cells to TNG348 treatment. Consistent with these findings, combination of TNG348 with PARPi leads to synergistic anti-tumor effects in HRD tumors, resulting in tumor growth inhibition and regression in multiple mouse xenograft tumor models. Importantly, our data in human cancer models further show that the addition of TNG348 to PARPi treatment can overcome acquired PARPi resistance in vivo. While the clinical development of TNG348 has been discontinued due to unexpected liver toxicity in patients (NCT06065059), the present data provides preclinical and mechanistic support for the continued exploration of USP1 as a drug target for the treatment of patients with BRCA1/2 mutant or HRD cancers.


  • Organizational Affiliation

    Tango Therapeutics (United States), Boston, MA, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinA [auth C]75Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 48B [auth D]685Homo sapiensMutation(s): 0 
Gene Names: WDR48KIAA1449UAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3
GTEx:  ENSG00000114742 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAF3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1C [auth E]786Homo sapiensMutation(s): 2 
Gene Names: USP1
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94782 (Homo sapiens)
Explore O94782 
Go to UniProtKB:  O94782
PHAROS:  O94782
GTEx:  ENSG00000162607 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94782
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BHF (Subject of Investigation/LOI)
Query on A1BHF

Download Ideal Coordinates CCD File 
F [auth E]2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8H-purin-8-imine
C27 H23 F6 N9 O
NKGSHRLGUQURMS-UHFFFAOYSA-N
A1A4Y
Query on A1A4Y

Download Ideal Coordinates CCD File 
D [auth C]3-(methanesulfonyl)propan-1-amine
C4 H11 N O2 S
QUYFSHOLLKVPGX-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3
MODEL REFINEMENTPHENIX1.18_3845

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references