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Yorodumi- PDB-5cy9: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cy9 | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / BRD4 / Bromodomain / Four Alpha Helices / BROMODOMAIN BINDING INHIBITOR / SIGNALING PROTEIN-INHIBITOR complex | ||||||
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 / 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 / Resolution: 1.55 Å | ||||||
Authors | Zhang, Y. / Song, M. / Liu, Z. / Xue, X. / Xu, Y. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery of Benzo[cd]indol-2(1H)-ones as Potent and Specific BET Bromodomain Inhibitors: Structure-Based Virtual Screening, Optimization, and Biological Evaluation Authors: Xue, X. / Zhang, Y. / Liu, Z. / Song, M. / Xing, Y. / Xiang, Q. / Wang, Z. / Tu, Z. / Zhou, Y. / Ding, K. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cy9.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cy9.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cy9_validation.pdf.gz | 805.4 KB | Display | wwPDB validaton report |
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Full document | 5cy9_full_validation.pdf.gz | 805.8 KB | Display | |
Data in XML | 5cy9_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5cy9_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cy9 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cy9 | HTTPS FTP |
-Related structure data
Related structure data | 5coiC 5cp5C 5cpeC 5cqtC 5crmC 5crzC 5cs8C 5ctlC 5d0cC 5dx4C 3mxfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16767.326 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60885 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | ChemComp-E0A / | ||
#4: Chemical | #5: 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: 2.57 Å3/Da / Density % sol: 52.13 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 20% PEG3350, 0.2M NaCl, 0.1M HEPES, 10% EtGhly,pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 0.97852 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.55→46.81 Å / Num. obs: 21754 / % possible obs: 90.5 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.023 / Net I/σ(I): 14.7 / Num. measured all: 169111 / Scaling rejects: 80 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXF Resolution: 1.55→46.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.391 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.081 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.902 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→46.81 Å
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Refine LS restraints |
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