+Open data
-Basic information
Entry | Database: PDB / ID: 6yqs | ||||||
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Title | BRD9 with methylpiperazinyl-benzyl-amino-dimethylpyridazinone | ||||||
Components | Bromodomain-containing protein 9 | ||||||
Keywords | TRANSCRIPTION / BRD9 / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN | ||||||
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 / chromatin / positive regulation of cell population proliferation / 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 / chromatin / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.683 Å | ||||||
Authors | Chung, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Application of Atypical Acetyl-lysine Methyl Mimetics in the Development of Selective Inhibitors of the Bromodomain-Containing Protein 7 (BRD7)/Bromodomain-Containing Protein 9 (BRD9) Bromodomains. Authors: Clegg, M.A. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Liwicki, G.M. / Michon, A.M. / Molnar, J. / Rioja, I. / Soden, P.E. / ...Authors: Clegg, M.A. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Liwicki, G.M. / Michon, A.M. / Molnar, J. / Rioja, I. / Soden, P.E. / Theodoulou, N.H. / Werner, T. / Tomkinson, N.C.O. / 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 | 6yqs.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yqs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/6yqs ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yqs | HTTPS FTP |
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-Related 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 Source method: isolated from a genetically manipulated source Details: 2,4-dimethyl-5-((2-(4-methylpiperazin-1-yl)benzyl)amino)pyridazin-3(2H)-one Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2 |
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#2: Chemical | ChemComp-P8Z / |
#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: 2.39 Å3/Da / Density % sol: 48.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.03M NaF, 0.03M NaI, 0.03M NaBr, 0.10M morpheus buffer 3 (1M pH 8.5), 37.5% morpheus MPD_P1K_3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.541 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→36.77 Å / Num. obs: 11735 / % possible obs: 91.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.017 / Net I/σ(I): 40.2 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.032 / Mean I/σ(I) obs: 20.6 / Num. unique obs: 1602 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.683→28.015 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.664 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.11 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.389 Å2
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Refinement step | Cycle: LAST / Resolution: 1.683→28.015 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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