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Yorodumi- PDB-5f25: Crystal structure of the BRD9 bromodomain in complex with compound 4. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f25 | |||||||||
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Title | Crystal structure of the BRD9 bromodomain in complex with compound 4. | |||||||||
Components | BRD9 | |||||||||
Keywords | TRANSCRIPTION / Bromodomain / Inhibitor | |||||||||
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 / regulation of transcription by RNA polymerase II / chromatin ...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 / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Bader, G. / Martin, L.J. / Steurer, S. / Weiss-Puxbaum, A. / Zoephel, A. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor. Authors: Martin, L.J. / Koegl, M. / Bader, G. / Cockcroft, X.L. / Fedorov, O. / Fiegen, D. / Gerstberger, T. / Hofmann, M.H. / Hohmann, A.F. / Kessler, D. / Knapp, S. / Knesl, P. / Kornigg, S. / ...Authors: Martin, L.J. / Koegl, M. / Bader, G. / Cockcroft, X.L. / Fedorov, O. / Fiegen, D. / Gerstberger, T. / Hofmann, M.H. / Hohmann, A.F. / Kessler, D. / Knapp, S. / Knesl, P. / Kornigg, S. / Muller, S. / Nar, H. / Rogers, C. / Rumpel, K. / Schaaf, O. / Steurer, S. / Tallant, C. / Vakoc, C.R. / Zeeb, M. / Zoephel, A. / Pearson, M. / Boehmelt, G. / McConnell, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f25.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f25.ent.gz | 86.8 KB | Display | PDB format |
PDBx/mmJSON format | 5f25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f25_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 5f25_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 5f25_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5f25_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/5f25 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/5f25 | HTTPS FTP |
-Related structure data
Related structure data | 5eu1C 5f1hC 5f1lC 5f2pC 3hmeS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: bromodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: glycerol ethoxylate, Tris |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.68→27.03 Å / Num. obs: 31467 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.013 / Net I/σ(I): 30.9 / Num. measured all: 197150 / Scaling rejects: 14 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HME Resolution: 1.68→27.03 Å / Cor.coef. Fo:Fc: 0.9511 / Cor.coef. Fo:Fc free: 0.9517 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.09
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Displacement parameters | Biso max: 105.82 Å2 / Biso mean: 38.09 Å2 / Biso min: 16.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.253 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→27.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.74 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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