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

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Basic information

Entry
Database: PDB / ID: 8oua
TitleCereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11f
Components(Cereblon isoform ...) x 2
KeywordsSIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue
Function / homologyCULT domain / CULT domain profile. / metal ion binding / PHOSPHATE ION / Chem-W0Z / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)36,2209
Polymers35,3023
Non-polymers9186
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-23 kcal/mol
Surface area14410 Å2
Unit cell
Length a, b, c (Å)56.422, 59.472, 88.147
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-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A20 - 122
122A20 - 123
133A19 - 123

NCS ensembles :
ID
1
2
3

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Components

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Cereblon isoform ... , 2 types, 3 molecules ABC

#1: Protein Cereblon isoform 4


Mass: 11748.402 Da / Num. of mol.: 2
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: Protein Cereblon isoform 4


Mass: 11805.455 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 84 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-W0Z / 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(fluoranyl)-3-methoxy-benzamide


Mass: 313.257 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13F2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.81 Å3/Da / Density % sol: 31.97 %
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: Aug 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→49.3 Å / Num. obs: 25046 / % possible obs: 96.4 % / Redundancy: 12 % / CC1/2: 0.998 / Net I/σ(I): 11.62
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 3258 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.898 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.145
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.238 1259 5.027 %
Rwork0.184 --
obs-25046 96.4 %
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: 38.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.524 Å20 Å20 Å2
2--0.109 Å20 Å2
3---0.414 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 52 78 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0112460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162099
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.633372
X-RAY DIFFRACTIONr_angle_other_deg0.6741.5634806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.8367.63219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97410290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
X-RAY DIFFRACTIONr_nbd_refined0.1940.2364
X-RAY DIFFRACTIONr_nbd_other0.2260.277
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21166
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.212
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_it5.6294.0741249
X-RAY DIFFRACTIONr_mcbond_other5.6244.0741249
X-RAY DIFFRACTIONr_mcangle_it6.77.2651562
X-RAY DIFFRACTIONr_mcangle_other6.7017.2681563
X-RAY DIFFRACTIONr_scbond_it6.9994.451211
X-RAY DIFFRACTIONr_scbond_other6.814.4451208
X-RAY DIFFRACTIONr_scangle_it9.4177.9881805
X-RAY DIFFRACTIONr_scangle_other9.057.9731800
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: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 69 -
Rwork0.372 1304 -
obs--72.95 %

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