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- PDB-7v1u: Crystal Structure of the first bromodomain of human BRD4 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v1u | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZJ12 | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | PROTEIN BINDING / BRD4(1) / Bromodomain | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-5E3 / Alpha-amanitin proprotein 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, M. / Wang, C. / Zhang, C. / Zhang, Y. / Xu, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design, synthesis and pharmacological characterization of N-(3-ethylbenzo[d]isoxazol-5-yl) sulfonamide derivatives as BRD4 inhibitors against acute myeloid leukemia. Authors: Zhang, M.F. / Luo, X.Y. / Zhang, C. / Wang, C. / Wu, X.S. / Xiang, Q.P. / Xu, Y. / Zhang, 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 | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 29.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7v2jC ![]() 5z1sS 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: 16767.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 28-43 are His-tag and thrombin cleavage site. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-5E3 / ~{ |
#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: 1.93 Å3/Da / Density % sol: 36.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 30% PEG5000, 0.2M (NH4)2SO4, 0.1M MES monohydrate, PH6.5 |
-Data collection
Diffraction | Mean temperature: 193 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: 0.97852 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.82→40.05 Å / Num. obs: 12201 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.034 / Rrim(I) all: 0.096 / Net I/σ(I): 13.9 / Num. measured all: 99072 / Scaling rejects: 887 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Resolution: 1.82→1.86 Å
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Z1S Resolution: 1.82→40.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.508 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.156 / 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: 60.99 Å2 / Biso mean: 22.55 Å2 / Biso min: 11.06 Å2
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Refinement step | Cycle: final / Resolution: 1.82→40.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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