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Open data
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Basic information
Entry | Database: PDB / ID: 5y93 | ||||||
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Title | Crystal Structure Analysis of the BRD4 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / BRD4(1) / Bromodomain | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, Y. / Zhang, Y. / Song, M. / Wang, C. | ||||||
![]() | ![]() Title: Structure-Based Discovery and Optimization of Benzo[ d]isoxazole Derivatives as Potent and Selective BET Inhibitors for Potential Treatment of Castration-Resistant Prostate Cancer (CRPC) Authors: Zhang, M. / Zhang, Y. / Song, M. / Xue, X. / Wang, J. / Wang, C. / Zhang, C. / Li, C. / Xiang, Q. / Zou, L. / Wu, X. / Wu, C. / Dong, B. / Xue, W. / Zhou, Y. / Chen, H. / Wu, D. / Ding, K. / Xu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 31.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769 KB | Display | ![]() |
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Full document | ![]() | 769.2 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16767.326 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168 Source method: isolated from a genetically manipulated source Details: sequence from 28-43 are tags. MKKGHHHHHHLVPRGS / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 72 molecules ![](data/chem/img/8Q9.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-8Q9 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH8.3 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→78.03 Å / Num. obs: 17128 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.62→1.64 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.307 / Num. unique obs: 823 / CC1/2: 0.968 / Rpim(I) all: 0.128 / Rrim(I) all: 0.333 / % possible all: 99.9 |
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Processing
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Refinement | Resolution: 1.62→40.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.822 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.097 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.18 Å2 / Biso mean: 19.216 Å2 / Biso min: 9.69 Å2
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Refinement step | Cycle: final / Resolution: 1.62→40.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.617→1.659 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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