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- PDB-6vn2: USP7 IN COMPLEX WITH LIGAND COMPOUND 18 -

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Basic information

Entry
Database: PDB / ID: 6vn2
TitleUSP7 IN COMPLEX WITH LIGAND COMPOUND 18
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 / 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
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
ACETATE ION / Chem-R44 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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 2.0Jun 17, 2020Group: Non-polymer description / Structure summary / Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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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)82,0335
Polymers80,9512
Non-polymers1,0813
Water19811
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0463
Polymers40,4761
Non-polymers5702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9872
Polymers40,4761
Non-polymers5111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.044, 65.339, 85.081
Angle α, β, γ (deg.)90.000, 93.860, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A207 - 553
2010B207 - 553

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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: 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-R44 / 1-({7-[(2R)-5-chloro-2-(piperazine-1-carbonyl)-2,3-dihydro-1-benzofuran-7-yl]thieno[3,2-b]pyridin-2-yl}methyl)-1H-pyrrole-2,5-dione


Mass: 510.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23ClN4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.5 Å3/Da / Density % sol: 50 %
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: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.93→84.89 Å / Num. obs: 15837 / % possible obs: 94.7 % / Redundancy: 2.3 % / Biso Wilson estimate: 76.792 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.083 / Χ2: 0.938 / Net I/σ(I): 10.14 / Num. measured all: 37169 / Scaling rejects: 692
Reflection shellResolution: 2.93→3.18 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Num. measured obs: 156 / Num. possible: 76 / Num. unique obs: 3429 / CC1/2: 0.895 / Rrim(I) all: 0.05 / % possible all: 95

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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 / Resolution: 2.93→47.8 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 54.566 / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 624 3.9 %RANDOM
Rwork0.2219 ---
obs0.2245 15212 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 203.95 Å2 / Biso mean: 92.042 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.13 Å20 Å2-1.05 Å2
2---0.48 Å2-0 Å2
3---6.69 Å2
Refinement stepCycle: final / Resolution: 2.93→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5507 0 74 14 5595
Biso mean--86.12 42.31 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195452
X-RAY DIFFRACTIONr_bond_other_d0.0030.024975
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.977412
X-RAY DIFFRACTIONr_angle_other_deg1.245311380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5895676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51824.942257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8751522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026295
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021245
Refine LS restraints NCS

Ens-ID: 1 / Number: 20080 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.93→3.006 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.547 38 -
Rwork0.323 1114 -
all-1152 -
obs--94.43 %
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)
15.253-0.98450.24933.69330.84893.36810.15550.5135-0.4186-0.2071-0.00070.0308-0.3409-0.1789-0.15490.24140.02010.0940.49650.01470.088317.678-0.30540.027
28.08941.71191.12225.59120.71670.20630.3022-0.37120.43970.2304-0.2683-1.17430.0947-0.0203-0.0340.4853-0.0215-0.05940.8280.15680.675548.6773.73251.099
35.23431.8092-5.61720.8669-0.50514.82980.26790.18340.09450.04250.0846-0.0536-0.60.2925-0.35240.62610.0690.08280.67960.10720.821138.7060.91524.075
48.0882-1.51193.07860.382-0.58831.17520.30010.714-0.443-0.1742-0.10740.34460.15520.2971-0.19280.78430.1813-0.08370.77670.09520.8076-4.11213.58239.598
55.25210.4578-1.38484.4793-1.11612.9132-0.0007-0.2246-0.28420.3251-0.0476-0.1627-0.17470.18660.04840.394-0.01090.0920.422300.04847.0913.03178.653
67.4752-3.6033-3.65971.78461.37096.1598-0.00540.0958-0.17150.0614-0.05340.14850.0411-0.37520.05880.4711-0.07380.16020.5763-0.08760.628-24.3167.15987.125
79.1337-2.3366-1.55412.79373.74725.3842-0.0659-0.20720.1697-0.05180.1413-0.0292-0.13260.1915-0.07530.65820.00190.06820.63260.01480.5917-3.5483.076102.425
86.73121.5114-1.59984.17642.42396.37180.05210.01810.5167-0.4460.3985-1.4957-0.75161.5267-0.45070.5201-0.15840.10570.91370.09420.894824.66517.27966.552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A207 - 326
2X-RAY DIFFRACTION1A347 - 367
3X-RAY DIFFRACTION1A396 - 408
4X-RAY DIFFRACTION1A421 - 533
5X-RAY DIFFRACTION2A327 - 346
6X-RAY DIFFRACTION2A368 - 395
7X-RAY DIFFRACTION3A409 - 420
8X-RAY DIFFRACTION4A534 - 554
9X-RAY DIFFRACTION5B207 - 326
10X-RAY DIFFRACTION5B347 - 367
11X-RAY DIFFRACTION5B396 - 408
12X-RAY DIFFRACTION5B421 - 533
13X-RAY DIFFRACTION6B327 - 346
14X-RAY DIFFRACTION6B368 - 395
15X-RAY DIFFRACTION7B409 - 420
16X-RAY DIFFRACTION8B534 - 553

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