9M3N | pdb_00009m3n

Crystal structure of human TRIM21 PRYSPRY in complex with T-02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.189 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

TRIM21-Driven Degradation of BRD4: Development of Heterobifunctional Degraders and Investigation of Recruitment and Selectivity Mechanisms.

Zhang, L.Wang, Q.Li, X.Cheng, X.Cai, L.Guo, A.Zhang, L.Hu, H.Wu, M.Li, X.Li, H.Meng, X.Qiu, Y.Tu, G.Zhang, L.Dong, X.Liang, Y.Wang, Y.Li, J.Dou, D.Pu, X.

(2025) J Chem Inf Model 65: 7584-7604

  • DOI: https://doi.org/10.1021/acs.jcim.5c00473
  • Primary Citation of Related Structures:  
    9M3N

  • PubMed Abstract: 

    TRIM21 is a highly efficient and versatile E3 ubiquitin ligase that plays a crucial role in targeted protein degradation through its specific binding capabilities. To investigate its role in chemically mediated degradation, we utilized two high-affinity binders identified from a DNA-encoded compound library (DEL) to design and synthesize several TrimTACs (TRIM21-based degraders) targeting BRD4. Degradation assays revealed that TrimTACs incorporating distinct TRIM21-binding moieties produced markedly different levels of BRD4 degradation. Further, to elucidate mechanisms underlying ternary complex formation and selective degradation, we employed precise ternary complex modeling combined with Gaussian accelerated molecular dynamics (GaMD) simulations. These computational analyses demonstrated that the diversity of TRIM21-binding moieties significantly affects the stability and conformation of the complex. Structurally stable complexes efficiently induce BRD4 degradation, and the binding orientation of BRD4 directly affects ubiquitin transfer and degradation efficiency. Moreover, key residues critical for complex formation were identified, shedding light on the cooperative interactions driving TRIM21-mediated degradation. Building on these findings, we conducted degradation experiments to validate novel TrimTAC designs derived from our ternary complex-based free energy perturbation (FEP) calculations. The results confirmed the reliability and accuracy of the ternary complex model, providing key insights for the rational design and optimization of TrimTACs, thereby advancing the development of targeted protein degraders.


  • Organizational Affiliation
    • HitGen Inc., Chengdu 610200, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21180Homo 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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EMT (Subject of Investigation/LOI)
Query on A1EMT

Download Ideal Coordinates CCD File 
B [auth A]1-ethyl-~{N}-methyl-5-phenyl-~{N}-[3-[3-(trifluoromethyl)phenyl]cyclobutyl]pyrazole-4-carboxamide
C24 H24 F3 N3 O
VWSNDEZRLZHMNM-PUZFROQSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.189 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.04α = 90
b = 100.04β = 90
c = 50.7γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references