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Yorodumi- PDB-7rxr: Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rxr | |||||||||
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Title | Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine | |||||||||
Components | Bromodomain-containing protein 4 | |||||||||
Keywords | GENE REGULATION/INHIBITOR / BRD4 / GENE REGULATION / GENE REGULATION-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: 1.41 Å | |||||||||
Authors | Cui, H. / Johnson, J.A. / Shi, K. / Aihara, H. / Pomerantz, W.C.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. Authors: Cui, H. / Divakaran, A. / Hoell, Z.J. / Ellingson, M.O. / Scholtz, C.R. / Zahid, H. / Johnson, J.A. / Griffith, E.C. / Gee, C.T. / Lee, A.L. / Khanal, S. / Shi, K. / Aihara, H. / Shah, V.H. ...Authors: Cui, H. / Divakaran, A. / Hoell, Z.J. / Ellingson, M.O. / Scholtz, C.R. / Zahid, H. / Johnson, J.A. / Griffith, E.C. / Gee, C.T. / Lee, A.L. / Khanal, S. / Shi, K. / Aihara, H. / Shah, V.H. / Lee, R.E. / Harki, D.A. / Pomerantz, W.C.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rxr.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rxr.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 7rxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rxr_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7rxr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7rxr_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7rxr_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/7rxr ftp://data.pdbj.org/pub/pdb/validation_reports/rx/7rxr | HTTPS FTP |
-Related structure data
Related structure data | 7r9cC 7rxsC 7rxtC 7jt4S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 2 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 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→111.44 Å / Num. obs: 54825 / % possible obs: 99.7 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.41→1.43 Å / Rmerge(I) obs: 0.726 / Num. unique obs: 2590 / CC1/2: 0.655 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7jt4 Resolution: 1.41→55.72 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.7859 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→55.72 Å
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Refine LS restraints |
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LS refinement shell |
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