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Yorodumi- PDB-5u69: Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-met... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u69 | ||||||
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Title | Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine | ||||||
Components | Polycomb protein EED | ||||||
Keywords | PROTEIN BINDING / INHIBITOR / WD40 PRC2 | ||||||
Function / homology | Function and homology information ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / HCMV Early Events ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / HCMV Early Events / PKMTs methylate histone lysines / heterochromatin formation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / 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: 1.28 Å | ||||||
Authors | Jakob, C.G. / Zhu, H. | ||||||
Citation | Journal: Bioorg. Med. Chem. Lett. / Year: 2017 Title: SAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding. Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / ...Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / Algire, M.A. / He, Y. / Richardson, P.L. / Sweis, R.F. / Sun, C. / Chiang, G.G. / Michaelides, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u69.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u69.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 5u69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u69_validation.pdf.gz | 808.4 KB | Display | wwPDB validaton report |
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Full document | 5u69_full_validation.pdf.gz | 808.4 KB | Display | |
Data in XML | 5u69_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5u69_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/5u69 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/5u69 | HTTPS FTP |
-Related structure data
Related structure data | 5u6dC 5u8aC 5u8fC 5k0mS C: citing same article (ref.) S: Starting model for refinement |
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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: 42583.484 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 | ChemComp-LQD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 8.5 Details: 3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→62.58 Å / Num. obs: 118159 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K0M Resolution: 1.28→62.58 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.198 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.733 Å2
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Refinement step | Cycle: 1 / Resolution: 1.28→62.58 Å
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Refine LS restraints |
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