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- PDB-8gq0: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with STL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gq0 | |||||||||
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Title | Crystal structure of BRD4 bromodomain 1 (BD1) in complex with STL233497 | |||||||||
![]() | Bromodomain-containing protein 4 | |||||||||
![]() | TRANSCRIPTION / BD1 / complex / inhibitor | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Park, T.H. / Lee, B.I. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study. Authors: Kim, J.H. / Pandit, N. / Yoo, M. / Park, T.H. / Choi, J.U. / Park, C.H. / Jung, K.Y. / Lee, B.I. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 10.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ymgC ![]() 7yq9C ![]() 8gpzC ![]() 6keiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14754.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 97 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KCL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/KCL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-KCL / ~{ | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.43 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 6 M Sodium formate, 10% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 22530 / % possible obs: 98.5 % / Redundancy: 6.1 % / CC1/2: 1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Rsym value: 0.066 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.44→1.46 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 924 / CC1/2: 0.838 / Rpim(I) all: 0.273 / Rrim(I) all: 0.647 / Rsym value: 0.584 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6kei Resolution: 1.44→40.803 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.55 / Stereochemistry target values: ML
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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 max: 40.1 Å2 / Biso mean: 15.3462 Å2 / Biso min: 8.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.44→40.803 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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