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Yorodumi- PDB-7m16: Triazole-based BET family bromodomain inhibitor bound to BRD4(D1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7m16 | |||||||||
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Title | Triazole-based BET family bromodomain inhibitor bound to BRD4(D1) | |||||||||
Components | Bromodomain-containing protein 4 | |||||||||
Keywords | PROTEIN BINDING / 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 / 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 / Resolution: 1.42 Å | |||||||||
Authors | Johnson, J.A. / Pomerantz, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: ACS Med. Chem. Lett. / Year: 2019 Title: Systematically Mitigating the p38alpha Activity of Triazole-based BET Inhibitors Authors: Carlson, A.S. / Cui, H. / Divakaran, A. / Johnson, J.A. / Brunner, R.M. / Pomerantz, W.C.K. / Topczewski, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m16.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m16.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 7m16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m16_validation.pdf.gz | 788.2 KB | Display | wwPDB validaton report |
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Full document | 7m16_full_validation.pdf.gz | 789.2 KB | Display | |
Data in XML | 7m16_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7m16_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/7m16 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/7m16 | HTTPS FTP |
-Related structure data
Related structure data | 3mxfS 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: 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 BL21(DE3) (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-YNS / |
#3: 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: 2.04 Å3/Da / Density % sol: 39.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium nitrate, 20% (v/v) PEG 3350 and 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.418→30.53 Å / Num. obs: 23920 / % possible obs: 98.61 % / Redundancy: 4.8 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.07137 / Rrim(I) all: 0.07981 / Net I/σ(I): 19.55 |
Reflection shell | Resolution: 1.418→1.469 Å / Rmerge(I) obs: 0.4634 / Num. unique obs: 2279 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mxf Resolution: 1.42→30.53 Å / SU ML: 0.1423 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 22.4656 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: 16.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→30.53 Å
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Refine LS restraints |
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LS refinement shell |
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