9LYF: Ubiquitin carboxyl-terminal hydrolase 30

Name: PDB 9LYF: Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30
Published: 2025-05-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30. Determined by X-ray diffraction at 2.58 Å resolution. Released 21 May 2025.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,316
Mol. weight: 38.86 kDa
Ligands: A1L7W, ZN
Released: 21 May 2025

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

Secondary structure: helices and β-sheets

9LYF contains 16 α-helices and 21 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: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	69-70	2	1
α-helix	77-86	10
α-helix	90-100	11
α-helix	116-127	12
β-strand	137-138	2	1
α-helix	141-149	9
α-helix	162-177	16
α-helix	220-222	3
β-strand	226-234	9	2
α-helix	239	1
β-strand	240	1	2
α-helix	241-243	3
β-strand	244-248	5	2
β-strand	251-253	3	3
β-strand	259	1	4
β-strand	262	1	4
β-strand	265	1	5
α-helix	266-275	10
β-strand	277-279	3	2
α-helix	285-291	7
α-helix	302-305	4
β-strand	308-314	7	2
α-helix	317-318	2
β-strand	320-325	6	3
β-strand	328-330	3	6
β-strand	336-338	3	6
β-strand	344	1	5
β-strand	348-349	2	3
α-helix	352-354	3
β-strand	436-445	10	3
β-strand	452-458	7	3
α-helix	459-461	3
α-helix	469-470	2
β-strand	473-477	5	3
β-strand	480-484	5	3
α-helix	486-490	5
β-strand	494-501	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 30	A	protein	336	Homo sapiens	Q70CQ3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9LYF_1 Ubiquitin carboxyl-terminal hydrolase 30 (chains A)
GPKGLVPGLVNLGNTCFMNSLLQGLSACPAFIRWLEEFTSQYSRDQKEPPSHQYLSLTLL
HLLKALSCQEVTDDEVLDASCLLDVLRMYRWQISSFEEQDAHELFHVITSSLEDERDGSG
SHWKSQHPFHGRLTSNMVCKHCEHQSPVRFDTFDSLSLSIPAATWGHPLTLDHCLHHFIS
SESVRDVVCDNCTKIEAKGTLNGEKVEHQRTTFVKQLKLGKLPQCLCIHLQRLSWSSHGT
PLKRHEHVQFNEDLSMDEYKYHSNASTYLFRLMAVVVHHGDMHSGHFVTYRRSPPSARNP
LSTSNQWLWVSDDTVRKASLQEVLSSSAYLLFYERV

Ligands and cofactors

ID	Name	Formula	Copies
A1L7W	5-(3-cyanophenyl)-~{N}-[[(3~{S})-1-(iminomethyl)pyrrolidin-3-yl]methyl]-1,3,4-o…	C16 H16 N6 O2	1
ZN	Zinc ion	Zn	1

Primary citation

Structure-based discovery of novel non-covalent small molecule inhibitors of USP30. Anbazhagan, P., Anantharajan, J., Fulwood, J. et al. J Comput Aided Mol Des (2025) 39:19-19. DOI 10.1007/s10822-025-00596-2 · PubMed

Other PDB entries of the same protein (UniProt Q70CQ3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
5OHK 2.34 Å, Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (high…
9F19 2.75 Å, Human USP30 chimera in complex with NK036 inhibitor
5OHP 2.8 Å, Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin
8D1T 2.94 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab
8D0A 3.19 Å, Crystal structure of human USP30 in complex with a covalent inhibitor 829 and a Fab
5OHN 3.6 Å, Crystal structure of USP30 in covalent complex with ubiquitin propargylamide (low…

Browse structure collections

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