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Yorodumi- PDB-4uiv: BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uiv | ||||||
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Title | BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4- oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c-pyridine-2- carboximidamide | ||||||
Components | BROMODOMAIN-CONTAINING PROTEIN 9 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER | ||||||
Function / homology | Function and homology information GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Chung, C. / Theodoulou, N.T. / Bamborough, P. / Humphreys, P.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: The Discovery of I-Brd9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / ...Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Michon, A. / Molnar, J. / Robson, S.C. / Tomkinson, N.C.O. / Kouzarides, T. / Prinjha, R.K. / Humphreys, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uiv.cif.gz | 60.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uiv.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uiv_validation.pdf.gz | 727.1 KB | Display | wwPDB validaton report |
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Full document | 4uiv_full_validation.pdf.gz | 727.6 KB | Display | |
Data in XML | 4uiv_validation.xml.gz | 9 KB | Display | |
Data in CIF | 4uiv_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uiv ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uiv | HTTPS FTP |
-Related structure data
Related structure data | 4uitC 4uiuC 4uiwC 4uixC 4uiyC 4uizC 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: 12228.203 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN OF BRD9, UNP RESIDUES 134-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9H8M2 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-XZB / |
#4: 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: 2.35 Å3/Da / Density % sol: 47.75 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6.5 Details: 0.1M MORPHEUS BUFFER PH 6.5, 30% MORPHEUS_EDO_P8K,0.1M MORPHEUS AMINO ACIDS 4C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 |
Detector | Date: Nov 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→28.22 Å / Num. obs: 10790 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 1.8 / % possible all: 83 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→28.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.387 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→28.22 Å
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