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- PDB-6uvm: Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uvm | ||||||
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Title | Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | GENE REGULATION/INHIBITOR / BRD4(D1) / inhibitor / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johnson, J.A. / Pomerantz, W.C.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 28 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 333.8 KB | Display | ![]() |
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Full document | ![]() | 333.8 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 3.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uvjC ![]() 6uwxC ![]() 3qzsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-QJA / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1 M bis-tris propane, 20% ethylene glycol, and 20% PEG3350 PH range: 6.5-7.0 / Temp details: ambient temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2019 |
Radiation | Monochromator: Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.509→39.16 Å / Num. obs: 20911 / % possible obs: 98.81 % / Redundancy: 5.1 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04872 / Rpim(I) all: 0.02333 / Rrim(I) all: 0.05425 / Net I/σ(I): 25.22 |
Reflection shell | Resolution: 1.509→1.563 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3294 / Mean I/σ(I) obs: 5.95 / Num. unique obs: 2056 / CC1/2: 0.886 / Rpim(I) all: 0.1593 / Rrim(I) all: 0.3673 / % possible all: 98.75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QZS Resolution: 1.51→39.16 Å / SU ML: 0.1485 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 19.2518
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→39.16 Å
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Refine LS restraints |
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LS refinement shell |
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