9QFY: CHIP E3 ubiquitin ligase TPR domain

Name: PDB 9QFY: Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 9.
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 9. Determined by X-ray diffraction at 1.06 Å resolution. Released 27 Aug 2025.

Method: X-ray diffraction
Resolution: 1.06 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,205
Mol. weight: 16.15 kDa
Ligands: A1I6I
Released: 27 Aug 2025

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

Secondary structure: helices and β-sheets

9QFY 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

>9QFY_1 E3 ubiquitin-protein ligase CHIP (chains A)
GSHMSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQ
ALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSA
LRIAKKKRWNSIEERR

Ligands and cofactors

ID	Name	Formula	Copies
A1I6I	~{N},~{N}-dimethyl-1-[(3~{S})-1-[[4,5,6,7-tetrakis(fluoranyl)-1~{H}-indol-3-yl]…	C17 H19 F4 N3 O3 S	1

Water and common crystallization additives (SO4) 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:

6NSV 1.3 Å, Crystal structure of the human CHIP TPR domain in complex with a 5mer acetylated…
9QFS 1.33 Å, Structure of CHIP E3 ubiquitin ligase TPR domain in complex with compound 8.
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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