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- PDB-7wln: Crystal Structure of the second bromodomain of human BRD2 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wln | ||||||
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Title | Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13153 | ||||||
![]() | Isoform 4 of Bromodomain-containing protein 2 | ||||||
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Function / homology | ![]() chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, J. / Zhang, C. / Xu, H. / Zhuang, X. / Wu, X. / Zhang, Y. / Xu, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Discovery and Optimization of Furo[3,2- c ]pyridin-4(5 H )-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors. Authors: Li, J. / Zhang, C. / Xu, H. / Wang, C. / Dong, R. / Shen, H. / Zhuang, X. / Chen, X. / Li, Q. / Lu, J. / Zhang, M. / Wu, X. / Loomes, K.M. / Zhou, Y. / Zhang, Y. / Liu, J. / 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 | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 84.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7wjsC ![]() 7wkyC ![]() 7wmqC ![]() 7wmuC ![]() 7wn5C ![]() 7wnaC ![]() 7wniC ![]() 6e6jS 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, 4 molecules ABCD
#1: Protein | Mass: 15981.218 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 73 molecules ![](data/chem/img/JFR.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JFR / #3: Chemical | ChemComp-DMS / | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-GOL / ![]() #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: 3.75 Å3/Da / Density % sol: 67.2 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 197 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→72.25 Å / Num. obs: 22992 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.091 / Rrim(I) all: 0.244 / Net I/σ(I): 6.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6E6J Resolution: 2.85→72.25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.059 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.84 Å2 / Biso mean: 49.128 Å2 / Biso min: 26.22 Å2
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Refinement step | Cycle: final / Resolution: 2.85→72.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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