9Q9P | pdb_00009q9p

TRIM21 PRYSPRY bound to compound 37

PDB DOI: https://doi.org/10.2210/pdb9Q9P/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.296 (Depositor), 0.313 (DCC)
R-Value Work:
0.232 (Depositor), 0.243 (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.

Macromolecule Content

Total Structure Weight: 23.05 kDa
Atom Count: 1,555
Modeled Residue Count: 184
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A [auth B]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19474
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I4X (Subject of Investigation/LOI) Query on A1I4X Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	(2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(2-methoxyphenyl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide C₃₀ H₄₁ N₅ O₄ ZDWZDLUIZUBTKV-DNZIZEQUSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.296 (Depositor), 0.313 (DCC)
R-Value Work: 0.232 (Depositor), 0.243 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.104	α = 90
b = 60.62	β = 113.01
c = 41.931	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.