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- PDB-8ou9: Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon ... -

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Basic information

Entry
Database: PDB / ID: 8ou9
TitleCereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11e
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-W1B / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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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)36,4029
Polymers35,4163
Non-polymers9866
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13 kcal/mol
Surface area14660 Å2
Unit cell
Length a, b, c (Å)56.328, 59.739, 88.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12A
13A

NCS domain segments:

Dom-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A

Component-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
11PROPRO19 - 1222 - 105
22ALAALA19 - 1232 - 106
33ALAALA19 - 1232 - 106

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cereblon isoform 4


Mass: 11805.455 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-W1B / 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-oxidanyl-benzamide


Mass: 263.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 32.28 %
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: 1.75→47.49 Å / Num. obs: 30740 / % possible obs: 100 % / Redundancy: 10.15 % / CC1/2: 0.998 / Net I/σ(I): 11.33
Reflection shellResolution: 1.75→1.81 Å / Num. unique obs: 4878 / CC1/2: 0.569

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→47.49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.994 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.224 1538 5.003 %
Rwork0.181 --
obs-30740 100 %
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: 32.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.324 Å20 Å20 Å2
2---0.41 Å20 Å2
3---1.734 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 60 89 2450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0112480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162110
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.6293392
X-RAY DIFFRACTIONr_angle_other_deg0.6891.5634831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.148.15819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59810284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02642
X-RAY DIFFRACTIONr_nbd_refined0.1980.2362
X-RAY DIFFRACTIONr_nbd_other0.2190.265
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21195
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.212
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_it4.9083.4621254
X-RAY DIFFRACTIONr_mcbond_other4.9093.4621254
X-RAY DIFFRACTIONr_mcangle_it6.1826.1681564
X-RAY DIFFRACTIONr_mcangle_other6.1816.171565
X-RAY DIFFRACTIONr_scbond_it5.7713.7821226
X-RAY DIFFRACTIONr_scbond_other5.7693.7841227
X-RAY DIFFRACTIONr_scangle_it7.7696.7541821
X-RAY DIFFRACTIONr_scangle_other7.7676.7551822
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 112 -
Rwork0.357 2090 -
obs--100 %

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