+Open data
-Basic information
Entry | Database: PDB / ID: 6w7f | ||||||
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Title | Structure of EED bound to inhibitor 5285 | ||||||
Components | Polycomb protein EED | ||||||
Keywords | GENE REGULATION / Inhibitor / Transcription-Inhibitor complex | ||||||
Function / homology | Function and homology information ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / chromosome / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Petrunak, E.M. / Stuckey, J.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: EEDi-5285: An Exceptionally Potent, Efficacious, and Orally Active Small-Molecule Inhibitor of Embryonic Ectoderm Development. Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Fernandez-Salas, E. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / ...Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Fernandez-Salas, E. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / Stuckey, J. / Zhou, Y. / Chen, J. / Tang, G. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7f.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7f.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7f ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7f | HTTPS FTP |
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-Related structure data
Related structure data | 6w7gC 2qxvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42412.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 4.3 M Sodium Formate, 18% Glycerol, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 23715 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 3 / Num. unique obs: 1170 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QXV Resolution: 2.2→24.59 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.16
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Displacement parameters | Biso max: 96.53 Å2 / Biso mean: 31.92 Å2 / Biso min: 5.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→24.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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