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Yorodumi- PDB-8ou9: Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ou9 | ||||||
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Title | Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 11e | ||||||
Components | Cereblon isoform 4 | ||||||
Keywords | SIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / Chem-W1B / Cereblon isoform 4 Function and homology information | ||||||
Biological species | Magnetospirillum gryphiswaldense (magnetotactic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Heim, C. / Bischof, L. / Hartmann, M.D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ou9.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ou9.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ou9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ou9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8ou9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8ou9_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 8ou9_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8ou9 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8ou9 | HTTPS FTP |
-Related structure data
Related structure data | 8ou3C 8ou4C 8ou5C 8ou6C 8ou7C 8ouaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Dom-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A
NCS ensembles :
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-Components
#1: Protein | 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 | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.28 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: 0.5 M (NH4)H2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.75→1.81 Å / Num. unique obs: 4878 / CC1/2: 0.569 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.31 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→47.49 Å
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Refine LS restraints |
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