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- PDB-8ou7: Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon ... -

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Basic information

Entry
Database: PDB / ID: 8ou7
TitleCereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11d
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-W1F / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHeim, C. / Bischof, L. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs.
Authors: Steinebach, C. / Bricelj, A. / Murgai, A. / Sosic, I. / Bischof, L. / Ng, Y.L.D. / Heim, C. / Maiwald, S. / Proj, M. / Voget, R. / Feller, F. / Kosmrlj, J. / Sapozhnikova, V. / Schmidt, A. / ...Authors: Steinebach, C. / Bricelj, A. / Murgai, A. / Sosic, I. / Bischof, L. / Ng, Y.L.D. / Heim, C. / Maiwald, S. / Proj, M. / Voget, R. / Feller, F. / Kosmrlj, J. / Sapozhnikova, V. / Schmidt, A. / Zuleeg, M.R. / Lemnitzer, P. / Mertins, P. / Hansen, F.K. / Gutschow, M. / Kronke, J. / Hartmann, M.D.
History
DepositionApr 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9269
Polymers40,8983
Non-polymers1,0286
Water1,53185
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9753
Polymers13,6331
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9753
Polymers13,6331
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9753
Polymers13,6331
Non-polymers3432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.409, 59.548, 88.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 20 - 123 / Label seq-ID: 20 - 123

Dom-IDComponent-IDEns-ID
111
211
322
422
533
633

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

#1: Protein Cereblon isoform 4


Mass: 13632.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-W1F / 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-methoxy-benzamide


Mass: 277.276 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H15N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.82 Å3/Da / Density % sol: 32.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.5 M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.554 Å / Num. obs: 33503 / % possible obs: 99.98 % / Redundancy: 12.85 % / CC1/2: 0.999 / Net I/σ(I): 14.74
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 5334 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.554 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.622 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2237 1676 5.008 %
Rwork0.1762 31789 -
all0.179 --
obs-33465 99.985 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.229 Å20 Å2-0 Å2
2--0.488 Å2-0 Å2
3----0.259 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 63 85 2443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0112466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162154
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.6323355
X-RAY DIFFRACTIONr_angle_other_deg0.6531.5694916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.0297.530
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.218103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56710314
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.73910103
X-RAY DIFFRACTIONr_chiral_restr0.110.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
X-RAY DIFFRACTIONr_nbd_refined0.1920.2336
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.21855
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21152
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.265
X-RAY DIFFRACTIONr_metal_ion_refined0.110.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1520.218
X-RAY DIFFRACTIONr_nbd_other0.2180.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0820.29
X-RAY DIFFRACTIONr_mcbond_it4.7813.7791212
X-RAY DIFFRACTIONr_mcbond_other4.7823.7791212
X-RAY DIFFRACTIONr_mcangle_it5.8386.7371510
X-RAY DIFFRACTIONr_mcangle_other5.8366.741511
X-RAY DIFFRACTIONr_scbond_it6.0934.2261254
X-RAY DIFFRACTIONr_scbond_other6.0914.2271255
X-RAY DIFFRACTIONr_scangle_it8.3467.541841
X-RAY DIFFRACTIONr_scangle_other8.3447.541842
X-RAY DIFFRACTIONr_lrange_it9.90142.1192656
X-RAY DIFFRACTIONr_lrange_other9.941.9652651
X-RAY DIFFRACTIONr_ncsr_local_group_10.1240.053043
X-RAY DIFFRACTIONr_ncsr_local_group_20.1150.052427
X-RAY DIFFRACTIONr_ncsr_local_group_30.1230.052421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.124340.05008
12AX-RAY DIFFRACTIONLocal ncs0.124340.05008
23AX-RAY DIFFRACTIONLocal ncs0.115330.05007
24AX-RAY DIFFRACTIONLocal ncs0.115330.05007
35AX-RAY DIFFRACTIONLocal ncs0.123080.05007
36AX-RAY DIFFRACTIONLocal ncs0.123080.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.3311240.33323260.33324500.8380.8211000.335
1.744-1.7920.3021160.27222180.27423340.9250.9391000.26
1.792-1.8440.2741150.23621910.23823060.9420.9581000.214
1.844-1.90.2561140.21121510.21322650.9560.9691000.185
1.9-1.9630.2491120.19320590.19621710.9630.9741000.165
1.963-2.0310.2161030.16620110.16821140.9720.9811000.14
2.031-2.1080.1881040.15619420.15820460.9770.9841000.132
2.108-2.1940.19990.14918590.15119580.9780.9861000.127
2.194-2.2910.174920.13618040.13818960.9820.9881000.117
2.291-2.4030.196900.14117270.14418170.9760.9881000.124
2.403-2.5320.211860.16916220.17217080.9740.9841000.151
2.532-2.6850.239830.18115720.18416550.9650.9811000.165
2.685-2.870.2770.16614690.16715460.9780.9831000.156
2.87-3.0990.215740.1613630.16214370.9680.9831000.157
3.099-3.3930.219660.16712660.1713320.9710.9831000.176
3.393-3.7920.192600.16311560.16512160.9790.9841000.176
3.792-4.3740.172550.15310350.15310900.980.9861000.173
4.374-5.3450.269460.1618790.1669260.9690.98499.8920.191
5.345-7.5120.3370.2457120.2487500.9570.96699.86670.285
7.512-47.5540.29230.2334220.2354470.9570.96499.55260.284

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