9N9Y | pdb_00009n9y

Crystal structure of truncated USP1:UAF1 in complex with compound 18


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.291 (Depositor), 0.292 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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Literature

Discovery of TNG-6132, a potent, selective, and orally bioavailable USP1 inhibitor.

Throner, S.Feng, T.Andersen, J.N.Bandi, M.Engel, J.L.Gong, S.Gotur, D.Gu, L.Huang, A.Lazarides, K.Maxwell, J.P.McCarren, P.McMillan, B.J.Pham, T.V.Simoneau, A.Tsai, A.Whittington, D.A.Wilker, E.Zhang, M.Zhang, W.

(2025) Bioorg Med Chem Lett 124: 130262-130262

  • DOI: https://doi.org/10.1016/j.bmcl.2025.130262
  • Primary Citation of Related Structures:  
    9N9Y

  • PubMed Abstract: 

    USP1 (ubiquitin-specific peptidase 1) is a deubiquitinating enzyme that has been identified as essential in BRCA1/2 mutant cells and implicated in the DNA damage response. Inhibition of USP1 by small molecule inhibitors disrupts DNA repair and replication and is being pursued as a potential anticancer therapeutic in BRCA1/2 mutant cancers. We report the discovery of an in vitro and in vivo USP1 inhibitor tool compound TNG-6132 (18), a reversible, allosteric inhibitor of USP1, which strongly inhibits USP1 enzymatic activity. This inhibitory effect translates into in vitro cellular viability defects in a BRCA1-mutant breast cancer cell line, as well as an in vivo pharmacodynamic (PD) response and tumor growth suppression in a mouse xenograft efficacy model. Additionally, we report an X-ray co-crystal structure of TNG-6132 (18) bound in the USP1-UAF1 complex, a result that furthered our understanding of the role played by key elements of the pharmacophore of this chemotype as well as its mechanism of inhibition of USP1.


  • Organizational Affiliation
    • Tango Therapeutics, 201 Brookline Ave, Boston, MA 02215, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 48569Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 1, N-terminal fragment,Ubiquitin carboxyl-terminal hydrolase 1381Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BWW (Subject of Investigation/LOI)
Query on A1BWW

Download Ideal Coordinates CCD File 
D [auth B]2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-7-({4-[1-methyl-4-(trifluoromethyl)-1H-imidazol-2-yl]phenyl}methyl)-5H-pyrrolo[3,2-d]pyrimidine
C26 H22 F3 N7 O
ONJHDRGRJAZAHT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.291 (Depositor), 0.292 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.2α = 90
b = 161.88β = 90
c = 160.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references