9Q9Q | pdb_00009q9q

TRIM21 PRYSPRY bound to compound 38

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.325 (Depositor), 0.316 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.245 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Development of TRIM21 PROTAC molecules

Luptak, J., James, L.C.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase TRIM21A [auth B],
B [auth A]		198Homo sapiensMutation(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 
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
A1I4Y (Subject of Investigation/LOI)
Query on A1I4Y
Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]		(2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(furan-2-yl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide
C27 H37 N5 O4
SXOXGCGOYIMWNS-LDVJMBRRSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.325 (Depositor), 0.316 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.245 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.905α = 90
b = 61.067β = 99.152
c = 67.269γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-08 
    • Deposition Author(s): Luptak, J.
Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

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