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- PDB-6vn6: USP7 IN COMPLEX WITH LIGAND COMPOUND 14 -

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Basic information

Entry
Database: PDB / ID: 6vn6
TitleUSP7 IN COMPLEX WITH LIGAND COMPOUND 14
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 / DUB / DEUBIQUITINASE
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 / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / 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 / negative regulation of gene expression via chromosomal CpG island methylation / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / 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
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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 ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-R4J / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLeger, P.R. / Wustrow, D.J. / Hu, D.X. / Krapp, S. / Maskos, K. / Blaesse, M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity.
Authors: Leger, P.R. / Hu, D.X. / Biannic, B. / Bui, M. / Han, X. / Karbarz, E. / Maung, J. / Okano, A. / Osipov, M. / Shibuya, G.M. / Young, K. / Higgs, C. / Abraham, B. / Bradford, D. / Cho, C. / ...Authors: Leger, P.R. / Hu, D.X. / Biannic, B. / Bui, M. / Han, X. / Karbarz, E. / Maung, J. / Okano, A. / Osipov, M. / Shibuya, G.M. / Young, K. / Higgs, C. / Abraham, B. / Bradford, D. / Cho, C. / Colas, C. / Jacobson, S. / Ohol, Y.M. / Pookot, D. / Rana, P. / Sanchez, J. / Shah, N. / Sun, M. / Wong, S. / Brockstedt, D.G. / Kassner, P.D. / Schwarz, J.B. / Wustrow, D.J.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 3, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)82,0996
Polymers80,9512
Non-polymers1,1484
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0503
Polymers40,4761
Non-polymers5742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0503
Polymers40,4761
Non-polymers5742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.301, 65.680, 85.313
Angle α, β, γ (deg.)90.000, 94.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 207 - 553 / Label seq-ID: 2 - 348

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 40475.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-R4J / [(2R)-5-chloro-7-{2-[(2S)-1-chloro-2,3-dihydroxypropan-2-yl]thieno[3,2-b]pyridin-7-yl}-2,3-dihydro-1-benzofuran-2-yl](piperazin-1-yl)methanone


Mass: 508.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23Cl2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→85.1 Å / Num. obs: 15436 / % possible obs: 97 % / Redundancy: 2.65 % / Biso Wilson estimate: 72.364 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.075 / Χ2: 0.953 / Net I/σ(I): 13.9
Reflection shellResolution: 2.99→3.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 3291 / CC1/2: 0.883 / Rrim(I) all: 0.029 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE MODEL

Resolution: 2.99→47.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 54.622 / SU ML: 0.444 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.492
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 590 3.8 %RANDOM
Rwork0.2194 ---
obs0.2212 14845 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.43 Å2 / Biso mean: 99.577 Å2 / Biso min: 47.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.44 Å2-0 Å23.62 Å2
2--1.48 Å20 Å2
3---2.42 Å2
Refinement stepCycle: final / Resolution: 2.99→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5470 0 68 0 5538
Biso mean--94.52 --
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195514
X-RAY DIFFRACTIONr_bond_other_d0.0020.025131
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9787463
X-RAY DIFFRACTIONr_angle_other_deg1.145311804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77124.944267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77515947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4881526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021243
Refine LS restraints NCS

Ens-ID: 1 / Number: 20178 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.99→3.068 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 51 -
Rwork0.322 1088 -
all-1139 -
obs--97.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6951-0.02710.27553.04470.41332.04090.11110.6901-0.0688-0.2039-0.0283-0.1538-0.3647-0.0118-0.08290.07690.03210.02730.14270.04280.051220.7421.1340.884
25.1276-0.2769-2.04942.4703-0.07792.64590.0251-0.5906-0.0250.4903-0.08760.2571-0.12480.24340.06250.241-0.03530.0210.16590.00270.12333.4084.79279.667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A207 - 555
2X-RAY DIFFRACTION2B207 - 553

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