9II5 | pdb_00009ii5

Crystal structure of human TRIM21 PRYSPRY in complex with compound 1

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-06-19 Released: 2025-05-07 
  • Deposition Author(s): Zhang, L.Y.
  • Funding Organization(s): Not funded

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Literature

Chemically Induced Nuclear Pore Complex Protein Degradation via TRIM21.

Li, X.Wang, Q.Guo, A.Qiu, Y.Chen, Q.Li, Y.Zhang, L.Guo, Y.Meng, X.Li, S.Liu, G.Zhang, L.Liu, J.Li, X.Cai, L.Cheng, X.Liu, C.Wang, X.Wood, A.Murray, J.Liu, G.Li, J.Huang, X.Dou, D.

(2025) ACS Chem Biol 

  • DOI: https://doi.org/10.1021/acschembio.4c00833
  • Primary Citation of Related Structures:  
    9II5

  • PubMed Abstract: 

    Despite the exciting progress of bifunctional degrader molecules, also known as proteolysis-targeting chimeras (PROTACs), the rapidly expanding field is still significantly hampered by the lack of available E3 ligase ligands. Our research bridges this gap by uncovering a series of small-molecule ligands to the E3 ligase TRIM21 through DNA-Encoded Library (DEL) technology. We confirmed their interaction with TRIM21 using crystallography and demonstrated their antiproliferative effects across various cancer cell types. Furthermore, proteomic studies identified that the mRNA Export Factor GLE1 and the Nuclear Pore Complex Protein NUP155 were significantly downregulated on TRIM21 ligand treatment. This degradation required TRIM21 and was ubiquitin-proteasome-dependent. More specifically, NUP155 was the primary target for the TRIM21 ligands, while GLE1 was considered a passenger target on initial degradation of NUP155. Using immunofluorescence techniques, we further demonstrated that the degradation of GLE1 and NUP155 proteins impaired the integrity of the nuclear envelope, leading to cell death. Highlighted by this research, a novel mode of action has been discovered for the TRIM21 E3 ligase ligand, acting as a monovalent degrader that triggers de novo interaction with functional complex proteins and induces their degradation.


  • Organizational Affiliation

    HitGen Inc., Chengdu, Sichuan 610200, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21178Homo sapiensMutation(s): 0 
Gene Names: TRIM21RNF81RO52SSA1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P19474 (Homo sapiens)
Explore P19474 
Go to UniProtKB:  P19474
PHAROS:  P19474
GTEx:  ENSG00000132109 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19474
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1D9F (Subject of Investigation/LOI)
Query on A1D9F

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[(1-fluoranylcyclohexyl)methyl]-~{N}-methyl-4-(2-methylsulfanylphenyl)-2-methylsulfonyl-benzamide
C23 H28 F N O3 S2
PAFGSEZHUCSUMW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.34α = 90
b = 65.34β = 90
c = 71.51γ = 120
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-05-07 
  • Deposition Author(s): Zhang, L.Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release