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Yorodumi- PDB-7jkz: Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jkz | ||||||
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Title | Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with YF3-126 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / Selective BRD4-BD1 inhibitor | ||||||
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: 2.49 Å | ||||||
Authors | Ratia, K.M. / Xiong, R. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Novel Pyrrolopyridone Bromodomain and Extra-Terminal Motif (BET) Inhibitors Effective in Endocrine-Resistant ER+ Breast Cancer with Acquired Resistance to Fulvestrant and Palbociclib. Authors: Li, Y. / Zhao, J. / Gutgesell, L.M. / Shen, Z. / Ratia, K. / Dye, K. / Dubrovskyi, O. / Zhao, H. / Huang, F. / Tonetti, D.A. / Thatcher, G.R.J. / Xiong, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jkz.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jkz.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jkz_validation.pdf.gz | 860.9 KB | Display | wwPDB validaton report |
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Full document | 7jkz_full_validation.pdf.gz | 861.5 KB | Display | |
Data in XML | 7jkz_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 7jkz_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/7jkz ftp://data.pdbj.org/pub/pdb/validation_reports/jk/7jkz | HTTPS FTP |
-Related structure data
Related structure data | 6p05C 7jkwC 7jkyC 2ouoS 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: 15060.332 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 BL21(DE3) (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-YF6 / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M (NH4)2SO4, 0.1M Na cacodylate pH 6.5, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→54.57 Å / Num. obs: 8677 / % possible obs: 99.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 958 / Rpim(I) all: 0.147 / Rrim(I) all: 0.466 / Χ2: 0.85 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUO Resolution: 2.49→54.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.741 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 131.5 Å2 / Biso mean: 50.905 Å2 / Biso min: 34.12 Å2
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Refinement step | Cycle: final / Resolution: 2.49→54.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.491→2.556 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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