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Yorodumi- PDB-6p05: Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p05 | ||||||
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Title | Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with compound 27 | ||||||
Components | Bromodomain-containing protein 4BRD4 | ||||||
Keywords | TRANSCRIPTION / inhibitor / brd4 / bromodomain | ||||||
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 / molecular replacement / Resolution: 1.54 Å | ||||||
Authors | Ratia, K.M. / Xiong, R. / Li, Y. / Zhao, J. / Gutgesell, L.M. / Shen, Z. / Dye, K. / Dubrovyskyii, O. / Zhao, H. / Huang, F. ...Ratia, K.M. / Xiong, R. / Li, Y. / Zhao, J. / Gutgesell, L.M. / Shen, Z. / Dye, K. / Dubrovyskyii, O. / Zhao, H. / Huang, F. / Tonetti, D.A. / 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 | 6p05.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p05.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/6p05 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/6p05 | HTTPS FTP |
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-Related structure data
Related structure data | 7jkwC 7jkyC 7jkzC 3mxfS 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: 15123.376 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 | #3: Chemical | ChemComp-YF2 / | #4: 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: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 16-18% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.54→19.84 Å / Num. obs: 22270 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.016 / Rrim(I) all: 0.06 / Net I/σ(I): 28.3 / Num. measured all: 296078 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MXF Resolution: 1.54→19.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.088 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0647 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.07 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.6 Å2 / Biso mean: 16.897 Å2 / Biso min: 8.59 Å2
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Refinement step | Cycle: final / Resolution: 1.54→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.535→1.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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