9EK5: TRIM21 PrySpry domain

TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog. Determined by X-ray diffraction at 2.1 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,549
Mol. weight: 20.92 kDa
Ligands: A1BLD
Released: 27 Aug 2025

Explore 9EK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EK5 contains 5 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	286	1	1
β-strand	291	1	2
β-strand	300-302	3	1
β-strand	308-311	4	1
β-strand	331-332	2	3
β-strand	333	1	2
β-strand	337	1	3
β-strand	341-347	7	1
β-strand	354-360	7	3
α-helix	373-375	3
β-strand	377-383	7	3
β-strand	387-390	4	3
β-strand	396-398	3	3
α-helix	403-404	2
β-strand	406-412	7	1
β-strand	417-422	6	1
α-helix	423-425	3
β-strand	428-433	6	1
β-strand	442-447	6	3
α-helix	459	1
β-strand	460-462	3	1
α-helix	463-464	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A	protein	181	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EK5_1 E3 ubiquitin-protein ligase TRIM21 (chains A)
SNAHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYW
EVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPP
CQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCP
L

Ligands and cofactors

ID	Name	Formula	Copies
A1BLD	(3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-…	C21 H22 Cl F N4 O2	1

Primary citation

Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex. Yuan, L., Ji, W., Dwyer, B.G. et al. Cancer Discov (2025) 15:2505-2529. DOI 10.1158/2159-8290.CD-25-0271 · PubMed

Other PDB entries of the same protein (UniProt P19474 (AlphaFold model), which also has an AlphaFold model), best resolution first:

32QO 1.3 Å, Human TRIM21 PRYSPRY domain in complex with compound 28 (Z38)
9PLM 1.32 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-021)
32QL 1.4 Å, Human TRIM21 PRYSPRY domain in complex with HGC652
9QBA 1.45 Å, Human TRIM21 PRYSPRY domain in complex with AL236
9II5 1.49 Å, Crystal structure of human TRIM21 PRYSPRY in complex with compound 1
32QM 1.5 Å, Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
8Y58 1.6 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine.
9PLL 1.6 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-056)
8Y5B 1.74 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.
32QN 1.8 Å, Human TRIM21 PRYSPRY domain in complex with compound 29 (Z37)
8Y59 1.89 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.
5OLM 1.95 Å, TRIM21

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