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- PDB-8ou3: Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon ... -

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Basic information

Entry
Database: PDB / ID: 8ou3
TitleCereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / PHOSPHATE ION / Chem-W1T / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsHeim, C. / Bischof, L. / Maiwald, S. / 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 21, 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)42,37412
Polymers41,1113
Non-polymers1,2639
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-25 kcal/mol
Surface area14470 Å2
Unit cell
Length a, b, c (Å)56.793, 59.519, 88.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Cereblon isoform 4


Mass: 13703.577 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

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Non-polymers , 5 types, 119 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EF2 / S-Thalidomide


Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-W1T / 4-azanyl-~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2-fluoranyl-benzamide


Mass: 265.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 32.12 %
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 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→49.33 Å / Num. obs: 51535 / % possible obs: 99.97 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 15.28
Reflection shellResolution: 1.47→1.523 Å / Mean I/σ(I) obs: 1.09 / Num. unique obs: 8199 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→49.327 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2378 2577 5 %
Rwork0.2147 48958 -
all0.216 --
obs-51535 99.973 %
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: 31.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.354 Å2-0 Å20 Å2
2--0.493 Å2-0 Å2
3----0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.47→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 75 110 2439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0112425
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6283305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.2275.74127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46110306
X-RAY DIFFRACTIONr_dihedral_angle_6_deg19.40410104
X-RAY DIFFRACTIONr_chiral_restr0.0820.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021928
X-RAY DIFFRACTIONr_nbd_refined0.2020.2908
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.30.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.28
X-RAY DIFFRACTIONr_mcbond_it2.0722.9991189
X-RAY DIFFRACTIONr_mcangle_it3.0895.3761479
X-RAY DIFFRACTIONr_scbond_it3.4623.3391236
X-RAY DIFFRACTIONr_scangle_it5.286.0031823
X-RAY DIFFRACTIONr_lrange_it6.41438.4063578
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
1.47-1.5080.3831860.35735440.35937360.8660.89799.83940.35
1.508-1.5490.3341850.32734890.32736740.920.9171000.31
1.549-1.5940.2791720.28433850.28435570.9420.941000.257
1.594-1.6430.2971780.26432890.26534670.9330.951000.232
1.643-1.6970.2431710.24431870.24433580.9570.961000.21
1.697-1.7570.2611650.21831000.2232650.9540.9681000.184
1.757-1.8230.2271590.21329860.21331450.9690.971000.18
1.823-1.8970.2151480.20528960.20630440.9680.9731000.174
1.897-1.9810.2141420.19327690.19429110.9710.9761000.169
1.981-2.0780.211390.226450.20127840.970.9751000.181
2.078-2.190.2371370.20325320.20526690.9660.9761000.189
2.19-2.3230.2161230.19824020.19925250.9730.9761000.187
2.323-2.4830.231160.19722650.19923810.9680.9761000.19
2.483-2.6810.2481160.22321010.22422170.9610.9691000.218
2.681-2.9360.2221000.22219580.22220580.9720.971000.227
2.936-3.2810.272930.2117630.21218560.9560.9721000.224
3.281-3.7860.194870.20115860.20116730.9770.9751000.23
3.786-4.630.206700.17913550.1814250.9750.9791000.214
4.63-6.5190.277560.2310630.23211190.9640.971000.288
6.519-49.3270.315340.2726430.2746850.9180.95798.83210.36

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