9Q9O | pdb_00009q9o

TRIM21 PRYSPRY bound to compound 36

• PDB DOI: https://doi.org/10.2210/pdb9Q9O/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-26 Released: 2025-10-08 
• Deposition Author(s): Luptak, J.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.368 (Depositor), 0.346 (DCC) 
• R-Value Work: 
  0.302 (Depositor), 0.276 (DCC) 

Starting Model: experimental

Literature

Development of TRIM21 PROTAC molecules

Luptak, J., James, L.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 92.16 kDa 
• Atom Count: 6,064 
• Modeled Residue Count: 732 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A [auth B], B [auth A], C, D	198	Homo sapiens	Mutation(s): 0  Gene Names: TRIM21, RNF81, RO52, SSA1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I4Z (Subject of Investigation/LOI)	E [auth B], F [auth A], G [auth C], H [auth D]	4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide C31 H32 N6 O2 BOWNAJGILQQXOM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.368 (Depositor), 0.346 (DCC) 
• R-Value Work:  0.302 (Depositor), 0.276 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.685	α = 90
b = 74.38	β = 90.103
c = 90.109	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Luptak, J.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release