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- PDB-8hje: Vismodegib binds to the catalytical domain of human Ubiquitin-Spe... -

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Basic information

Entry
Database: PDB / ID: 8hje
TitleVismodegib binds to the catalytical domain of human Ubiquitin-Specific Protease 28
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE / Vismodegib / USP28 / catalytical domain / inhibitor
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell population proliferation / Ub-specific processing proteases / nuclear body / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / 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 UIM domain / : / UBA-like domain / : / 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. / UBA-like superfamily / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-VIS / Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsShi, L. / Wang, H. / Xu, Z. / Xiong, B. / Zhang, N.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977105 China
National Natural Science Foundation of China (NSFC)21778061 China
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Structure-based discovery of potent USP28 inhibitors derived from Vismodegib.
Authors: Zhou, D. / Xu, Z. / Huang, Y. / Wang, H. / Zhu, X. / Zhang, W. / Song, W. / Gao, T. / Liu, T. / Wang, M. / Shi, L. / Zhang, N. / Xiong, B.
History
DepositionNov 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8542
Polymers44,4331
Non-polymers4211
Water00
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)105.099, 105.099, 327.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 44432.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is expressed as an insert deletion, and the catalytical domain of Ubiquitin-Specific protease 28 is linked by a flexible GSGSGS linker
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-VIS / 2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide


Mass: 421.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1 M Bis-tris propane pH 6.4, 0.2 M potassium thiocyanate, 20% PEG3350 and 3% sucrose

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.85→43.85 Å / Num. obs: 16695 / % possible obs: 99.58 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 20.76
Reflection shellResolution: 2.851→2.953 Å / Num. unique obs: 1629 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
REFMAC1.16refinement
xia2data scaling
xia2data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→43.85 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.84 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25429 825 4.9 %RANDOM
Rwork0.22206 ---
obs0.22372 15881 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.552 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20.79 Å2-0 Å2
2--1.58 Å2-0 Å2
3----5.14 Å2
Refinement stepCycle: 1 / Resolution: 2.85→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 27 0 2438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172182
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6333376
X-RAY DIFFRACTIONr_angle_other_deg1.2551.5774968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9465302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52522.426136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12715360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1671514
X-RAY DIFFRACTIONr_chiral_restr0.0640.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1847.4121236
X-RAY DIFFRACTIONr_mcbond_other6.1667.4121235
X-RAY DIFFRACTIONr_mcangle_it8.84311.081528
X-RAY DIFFRACTIONr_mcangle_other8.84611.0821529
X-RAY DIFFRACTIONr_scbond_it6.6587.4991260
X-RAY DIFFRACTIONr_scbond_other6.6567.51261
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.60711.1211849
X-RAY DIFFRACTIONr_long_range_B_refined11.99881.6752724
X-RAY DIFFRACTIONr_long_range_B_other11.99681.6672725
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.851→2.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 42 -
Rwork0.322 1170 -
obs--100 %

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