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- PDB-8ou3: Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ou3 | ||||||
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Title | Cereblon isoform 4 in complex with novel Benzamide-Type Cereblon Binder 8d | ||||||
![]() | Cereblon isoform 4 | ||||||
![]() | SIGNALING PROTEIN / Cereblon / PROTAC / E3 / molecular glue | ||||||
Function / homology | CULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / PHOSPHATE ION / Chem-W1T / Cereblon isoform 4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heim, C. / Bischof, L. / Maiwald, S. / Hartmann, M.D. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ou4C ![]() 8ou5C ![]() 8ou6C ![]() 8ou7C ![]() 8ou9C ![]() 8ouaC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 13703.577 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MGR_0879 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 119 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EF2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/W1T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EF2.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/W1T.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-W1T / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.12 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 27, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been used if present in the input file
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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: 31.333 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→49.327 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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