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- PDB-7wni: 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: 7wni | ||||||
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Title | Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13158 | ||||||
![]() | Isoform 4 of Bromodomain-containing protein 2 | ||||||
![]() | PROTEIN BINDING / BRD2-BD2 / Bromodomain / Inhibitor | ||||||
Function / homology | ![]() acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm 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 | ![]() | 63.5 KB | Display | ![]() |
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PDB format | ![]() | 44.8 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 ![]() 7wlnC ![]() 7wmqC ![]() 7wmuC ![]() 7wn5C ![]() 7wnaC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 15981.218 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BRD2_HUMAN, P25440, sequence from 320-343 are tags. EGDIHMKKGHHHHHHENLYFQGGS Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.77 Å3/Da / Density % sol: 67.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium malonate pH 4.0, 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: May 8, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.12→76.85 Å / Num. obs: 9140 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.798 / Rmerge(I) obs: 0.301 / Rpim(I) all: 0.136 / Rrim(I) all: 0.332 / Net I/σ(I): 4 / Num. measured all: 50495 / Scaling rejects: 106 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6E6J Resolution: 3.12→76.85 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.528 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.934 / ESU R Free: 0.386 / 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: 121.48 Å2 / Biso mean: 46.485 Å2 / Biso min: 13.12 Å2
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Refinement step | Cycle: final / Resolution: 3.12→76.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.12→3.201 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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