9LYF | pdb_00009lyf

Structure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30

• PDB DOI: https://doi.org/10.2210/pdb9LYF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-20 Released: 2025-05-21 
• Deposition Author(s): Anantharajan, J., Baburajendran, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.272 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Structure-based discovery of novel non-covalent small molecule inhibitors of USP30.

Anbazhagan, P., Anantharajan, J., Fulwood, J., Low, C.H., Baburajendran, N., Foo, K., Xu, W.

(2025) J Comput Aided Mol Des 39: 19-19

• PubMed: 40274689 
• DOI: https://doi.org/10.1007/s10822-025-00596-2
• Primary Citation of Related Structures:  
  9LYF


• PubMed Abstract: 
  

  Ubiquitin-specific proteases (USPs) are crucial regulators of protein degradation pathways, influencing diverse cellular processes and disease mechanisms. Among them, USP30 plays a pivotal role in mitochondrial quality control and has been implicated in idiopathic pulmonary fibrosis (IPF), a chronic lung disease for which current therapies merely slow disease progression. The high flexibility of USP30's catalytic site, coupled with its dependence on covalent interaction with the catalytic cysteine presents significant challenges in discovering suitable small molecule inhibitors. In this study, we identified three non-covalent small molecule inhibitors for USP30 using molecular modeling, X-ray crystallography, and virtual screening. These findings offer valuable insights and novel chemical starting points for further medicinal chemistry optimization.

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Organizational Affiliation: 
• Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, Singapore, 138670, Singapore.
Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, Singapore, 138670, Singapore. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.86 kDa 
• Atom Count: 2,316 
• Modeled Residue Count: 301 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 30	A	336	Homo sapiens	Mutation(s): 3  Gene Names: USP30 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q70CQ3 (Homo sapiens) Explore Q70CQ3  Go to UniProtKB:  Q70CQ3
PHAROS:  Q70CQ3 GTEx:  ENSG00000135093

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L7W (Subject of Investigation/LOI)	B [auth A]	5-(3-cyanophenyl)-~{N}-[[(3~{S})-1-(iminomethyl)pyrrolidin-3-yl]methyl]-1,3,4-oxadiazole-2-carboxamide C16 H16 N6 O2 WRBUPGZBRUFZCK-XACIZNRCSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.272 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.007	α = 90
b = 60.881	β = 90
c = 102.507	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Anantharajan, J., Baburajendran, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release