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Yorodumi- PDB-6uvj: Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uvj | ||||||
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Title | Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | GENE REGULATION/INHIBITOR / BRD4(D1) / inhibitor / 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 / 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: 1.38 Å | ||||||
Authors | Johnson, J.A. / Pomerantz, W.C.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 Title: Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains. Authors: Johnson, J.A. / Nicolaou, C.A. / Kirberger, S.E. / Pandey, A.K. / Hu, H. / 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 | 6uvj.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uvj.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 6uvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uvj_validation.pdf.gz | 345.3 KB | Display | wwPDB validaton report |
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Full document | 6uvj_full_validation.pdf.gz | 345.4 KB | Display | |
Data in XML | 6uvj_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6uvj_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/6uvj ftp://data.pdbj.org/pub/pdb/validation_reports/uv/6uvj | HTTPS FTP |
-Related structure data
Related structure data | 6uvmC 6uwxC 3qzsS 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: 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 | #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-QJ1 / | #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: 2.27 Å3/Da / Density % sol: 46 % / Description: Long rods, grew within 48 hours |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M bis-tris propane, 20 % PEG 3350 / PH range: 8.3-8.7 |
-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: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.378→38.56 Å / Num. obs: 27276 / % possible obs: 98.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.05466 / Rpim(I) all: 0.0273 / Rrim(I) all: 0.06142 / Net I/σ(I): 19.51 |
Reflection shell | Resolution: 1.378→1.427 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.2987 / Mean I/σ(I) obs: 5.28 / Num. unique obs: 2626 / Rpim(I) all: 0.1541 / Rrim(I) all: 0.3383 / % possible all: 96.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QZS Resolution: 1.38→38.56 Å / SU ML: 0.1032 / Cross valid method: NONE / Phase error: 17.6956
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→38.56 Å
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Refine LS restraints |
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LS refinement shell |
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