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- PDB-6m1k: USP7 in complex with a novel inhibitor -

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Basic information

Entry
Database: PDB / ID: 6m1k
TitleUSP7 in complex with a novel inhibitor
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Complex / USP7 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / rhythmic process / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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
Chem-EZF / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.255 Å
AuthorsLiu, S.J. / Zhou, X.Y. / Li, M.L. / Sun, H.B. / Wen, X.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81773584 China
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: N-benzylpiperidinol derivatives as novel USP7 inhibitors: Structure-activity relationships and X-ray crystallographic studies.
Authors: Li, M. / Liu, S. / Chen, H. / Zhou, X. / Zhou, J. / Zhou, S. / Yuan, H. / Xu, Q.L. / Liu, J. / Cheng, K. / Sun, H. / Wang, Y. / Chen, C. / Wen, X.
History
DepositionFeb 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4514
Polymers80,3492
Non-polymers1,1022
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area31740 Å2
Unit cell
Length a, b, c (Å)76.065, 69.200, 76.450
Angle α, β, γ (deg.)90.000, 95.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 40174.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-EZF / methyl 4-[[4-[[3-[4-(aminomethyl)phenyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-6-yl]methyl]-4-oxidanyl-piperidin-1-yl]methyl]-3-chloranyl-benzoate


Mass: 551.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31ClN6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris (hydroxymethyl)aminomethane hydrochloride, pH 7.0, 20% (v/v) PEG 1000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.255→41.18 Å / Num. obs: 35627 / % possible obs: 95.1 % / Redundancy: 6.3 % / CC1/2: 0.993 / Rpim(I) all: 0.074 / Rrim(I) all: 0.137 / Net I/σ(I): 21.3
Reflection shellResolution: 2.255→2.336 Å / Rmerge(I) obs: 0.075 / Num. unique obs: 3451

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3246refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N9T

5n9t


Resolution: 2.255→41.18 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.9
RfactorNum. reflection% reflection
Rfree0.269 1944 5.48 %
Rwork0.2331 --
obs0.2351 35489 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.85 Å2 / Biso mean: 52.9895 Å2 / Biso min: 29.84 Å2
Refinement stepCycle: final / Resolution: 2.255→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5437 0 78 164 5679
Biso mean--52.07 49.34 -
Num. residues----673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2554-2.31180.37481340.316229591
2.3118-2.37430.37941370.3251239896
2.3743-2.44420.37971400.3223239295
2.4442-2.52310.40711390.3216236795
2.5231-2.61320.34751380.3135239195
2.6132-2.71780.40271370.3017239795
2.7178-2.84150.33051340.3158234293
2.8415-2.99130.40171340.3296227991
2.9913-3.17860.34291380.2878233993
3.1786-3.42390.33541390.257241695
3.4239-3.76830.23921420.2161244597
3.7683-4.3130.21481460.1995244596
4.313-5.4320.18391370.1731246796
5.432-41.180.20951490.1769257299

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