+Open data
-Basic information
Entry | Database: PDB / ID: 6sb8 | ||||||
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Title | Crystal Structure of BRD4(1) bound to inhibitor BUX14 (7) | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / BRD4 / BRD4(1) / INHIBITOR / BROMODOMAIN / EPIGENETIC READER PROTEIN / ACETYLATED / LYSINE / HISTONE TAIL / PROTEIN BINDING-INHIBITOR COMPLEX / BUX14 / fragment | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Huegle, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: 4-Acyl Pyrroles as Dual BET-BRD7/9 Bromodomain Inhibitors Address BETi Insensitive Human Cancer Cell Lines. Authors: Hugle, M. / Regenass, P. / Warstat, R. / Hau, M. / Schmidtkunz, K. / Lucas, X. / Wohlwend, D. / Einsle, O. / Jung, M. / Breit, B. / Gunther, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sb8.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sb8.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 6sb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sb8_validation.pdf.gz | 931.2 KB | Display | wwPDB validaton report |
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Full document | 6sb8_full_validation.pdf.gz | 934 KB | Display | |
Data in XML | 6sb8_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 6sb8_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/6sb8 ftp://data.pdbj.org/pub/pdb/validation_reports/sb/6sb8 | HTTPS FTP |
-Related structure data
Related structure data | 6rwjC 6s4bC 6s6kC 6sa2C 6sa3C 6sahC 6sajC 4lywS S: Starting model for refinement 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: 15099.380 Da / Num. of mol.: 1 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-L45 / ~{ |
#3: Chemical | ChemComp-BU3 / ( |
#4: 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: 1.89 Å3/Da / Density % sol: 34.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaCl, PEG3350, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 4, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.12→47.75 Å / Num. obs: 42419 / % possible obs: 95 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.049 / Rrim(I) all: 0.141 / Net I/σ(I): 7.2 / Num. measured all: 330975 / Scaling rejects: 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LYW Resolution: 1.5→36.659 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.18 Å2 / Biso mean: 19.5263 Å2 / Biso min: 7.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→36.659 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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