9QFS: CHIP E3 ubiquitin ligase TPR domain

Name: PDB 9QFS: Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 8.
Published: 2025-08-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 8. Determined by X-ray diffraction at 1.33 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,138
Mol. weight: 16.11 kDa
Ligands: A1I6J
Released: 27 Aug 2025

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

Secondary structure: helices and β-sheets

9QFS contains 7 α-helices and 0 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	26-38	13
α-helix	42-55	14
α-helix	60-72	13
α-helix	76-89	14
α-helix	94-106	13
α-helix	110-126	17
α-helix	134-149	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase CHIP	A	protein	136	Homo sapiens	Q9UNE7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9QFS_1 E3 ubiquitin-protein ligase CHIP (chains A)
GSHMSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQ
ALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSA
LRIAKKKRWNSIEERR

Ligands and cofactors

ID	Name	Formula	Copies
A1I6J	~{N}-[(4~{R})-4-cyclohexyl-2,5-bis(oxidanylidene)imidazolidin-1-yl]-4,5,6,7-tet…	C18 H16 F4 N4 O3	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Discovery of Small-Molecule Ligands for the E3 Ligase STUB1/CHIP from a DNA-Encoded Library Screen. Lucas, S.C.C., Milbradt, A.G., Breed, J. et al. ACS Med Chem Lett (2025) 16:1445-1451. DOI 10.1021/acsmedchemlett.5c00361 · PubMed

Other PDB entries of the same protein (UniProt Q9UNE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9QFY 1.06 Å, Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 9.
6NSV 1.3 Å, Crystal structure of the human CHIP TPR domain in complex with a 5mer acetylated…
9QEU 1.35 Å, Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 1
8GCK 1.37 Å, Crystal structure of the human CHIP-TPR domain in complex with a 6mer acetylated tau…
8EI0 1.47 Å, Crystal structure of the STUB1 TPR domain in complex with H318, a Helicon Polypeptide
6EFK 1.5 Å, Crystal structure of the human CHIP TPR domain in complex with a 5mer acetylated HSP70…
9QF1 1.51 Å, Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 2
8F16 1.56 Å, Structure of the STUB1 TPR domain in complex with H203, an all-D Helicon Polypeptide
9DYB 1.6 Å, CHIP-TPR in complex with the phosphorylated Hsp70 tail
8SUV 1.63 Å, CHIP-TPR in complex with the C-terminus of CHIC2
8F14 1.69 Å, Structure of the STUB1 TPR domain in complex with H201, an all-D Helicon Polypeptide
8F15 1.73 Å, Structure of the STUB1 TPR domain in complex with H202, an all-D Helicon Polypeptide

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