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Yorodumi- PDB-7oeo: C-TERMINAL BROMODOMAIN OF HUMAN BRD4 N-(2,2-diphenylethyl)-4-meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oeo | ||||||
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Title | C-TERMINAL BROMODOMAIN OF HUMAN BRD4 N-(2,2-diphenylethyl)-4-methoxy-3,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)benzamide | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | NUCLEAR PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain / toxin activity / Chem-V9Z / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Chung, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of a Highly Selective BET BD2 Inhibitor from a DNA-Encoded Library Technology Screening Hit. Authors: Rianjongdee, F. / Atkinson, S.J. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Kaushansky, L.J. / Medeiros, P. / Messenger, C. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rioja, I. / Satz, ...Authors: Rianjongdee, F. / Atkinson, S.J. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Kaushansky, L.J. / Medeiros, P. / Messenger, C. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rioja, I. / Satz, A.L. / Taylor, S. / Wall, I.D. / Watson, R.J. / Yao, G. / Demont, E.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oeo.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oeo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oeo_validation.pdf.gz | 812.2 KB | Display | wwPDB validaton report |
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Full document | 7oeo_full_validation.pdf.gz | 812.2 KB | Display | |
Data in XML | 7oeo_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 7oeo_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/7oeo ftp://data.pdbj.org/pub/pdb/validation_reports/oe/7oeo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13636.714 Da / Num. of mol.: 1 / Fragment: UNP residues 347-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-V9Z / |
#3: 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: 2.82 Å3/Da / Density % sol: 56.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M Hepes pH7.5 and 20%w/v PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→33.64 Å / Num. obs: 23991 / % possible obs: 96.3 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.51→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1319 / CC1/2: 0.999 / % possible all: 73.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: in house structure Resolution: 1.51→33.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.474 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.075 / ESU R Free: 0.079 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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→33.64 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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