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- PDB-9lyf: Structure-based Discovery of Novel non-Covalent Small Molecule In... -

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Basic information

Entry
Database: PDB / ID: 9lyf
TitleStructure-based Discovery of Novel non-Covalent Small Molecule Inhibitors of USP30
ComponentsUbiquitin carboxyl-terminal hydrolase 30
KeywordsHYDROLASE / USP30 / deubiquitination / covalent small molecule inhibitor / non-Covalent Small Molecule Inhibitors
Function / homology
Function and homology information


protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / pexophagy / autophagy of mitochondrion / peroxisomal membrane / mitochondrial fusion / negative regulation of mitophagy / protein deubiquitination / Pexophagy ...protein K6-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / pexophagy / autophagy of mitochondrion / peroxisomal membrane / mitochondrial fusion / negative regulation of mitophagy / protein deubiquitination / Pexophagy / regulation of protein stability / ubiquitinyl hydrolase 1 / mitochondrial outer membrane / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleus / cytosol
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Ubiquitin carboxyl-terminal hydrolase 30
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsAnantharajan, J. / Baburajendran, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Comput.Aided Mol.Des. / Year: 2025
Title: Structure-based discovery of novel non-covalent small molecule inhibitors of USP30.
Authors: Anbazhagan, P. / Anantharajan, J. / Fulwood, J. / Low, C.H. / Baburajendran, N. / Foo, K. / Xu, W.
History
DepositionFeb 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8593
Polymers38,4691
Non-polymers3902
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.007, 60.881, 102.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 30 / Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 ...Deubiquitinating enzyme 30 / Ubiquitin thioesterase 30 / Ubiquitin-specific-processing protease 30 / Ub-specific protease 30


Mass: 38469.422 Da / Num. of mol.: 1 / Mutation: F348D,M350S,I353E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70CQ3, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-A1L7W / 5-(3-cyanophenyl)-~{N}-[[(3~{S})-1-(iminomethyl)pyrrolidin-3-yl]methyl]-1,3,4-oxadiazole-2-carboxamide


Mass: 324.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.58→47.08 Å / Num. obs: 10967 / % possible obs: 99.5 % / Redundancy: 5.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.103 / Rrim(I) all: 0.243 / Χ2: 0.45 / Net I/σ(I): 6.1 / Num. measured all: 59144
Reflection shellResolution: 2.58→2.69 Å / % possible obs: 96.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 1.41 / Num. measured all: 7123 / Num. unique obs: 1275 / CC1/2: 0.464 / Rpim(I) all: 0.642 / Rrim(I) all: 1.554 / Χ2: 0.36 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→47.08 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 1092 10.01 %
Rwork0.2216 --
obs0.2268 10909 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 1 16 2316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052353
X-RAY DIFFRACTIONf_angle_d0.7273198
X-RAY DIFFRACTIONf_dihedral_angle_d5.0431377
X-RAY DIFFRACTIONf_chiral_restr0.043375
X-RAY DIFFRACTIONf_plane_restr0.005404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.69590.36391300.30441173X-RAY DIFFRACTION97
2.6959-2.8380.33541350.27871210X-RAY DIFFRACTION100
2.838-3.01580.3331350.25381211X-RAY DIFFRACTION100
3.0158-3.24860.29891340.2551208X-RAY DIFFRACTION100
3.2486-3.57540.28651350.21161215X-RAY DIFFRACTION100
3.5754-4.09250.25631380.20721243X-RAY DIFFRACTION100
4.0925-5.15510.23861380.17561232X-RAY DIFFRACTION100
5.1551-47.080.24061470.2241325X-RAY DIFFRACTION100

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