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- PDB-7w3d: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w3d | ||||||
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Title | Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N2-(1,2,3-benzotriazol-5-yl)-N3-(dimethylsulfamoyl)-N6-[(2S)-1-methoxypropan-2-yl]pyridine-2,3,6-triamine | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | TRANSCRIPTION / protein-Inhibitor complex | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-89T / Alpha-amanitin proprotein 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, T.H. / Lee, B.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of BET specific bromodomain inhibitors with a novel scaffold. Authors: Pandit, N. / Yoo, M. / Hyun Park, T. / Kim, J. / Mi Kim, S. / Myung Lee, K. / Kim, Y. / Min Bong, S. / Il Lee, B. / Jung, K.Y. / Hoon Park, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.3 KB | Display | ![]() |
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PDB format | ![]() | 24.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ossS S: Starting model for refinement |
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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
#1: Protein | Mass: 15025.235 Da / Num. of mol.: 1 / Fragment: bromodomain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-89T / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.73 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 6M 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 EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 9173 / % possible obs: 95.8 % / Redundancy: 12.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Rsym value: 0.058 / Net I/σ(I): 43.28125 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.62 / Num. unique obs: 355 / CC1/2: 0.944 / CC star: 0.986 / Rpim(I) all: 0.238 / Rrim(I) all: 0.787 / Rsym value: 0.747 / % possible all: 74.9 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2OSS Resolution: 1.98→33.46 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.852 / SU B: 7.135 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.266 / 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: 58.91 Å2 / Biso mean: 28.293 Å2 / Biso min: 13.85 Å2
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Refinement step | Cycle: final / Resolution: 1.98→33.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.03 Å / Rfactor Rfree error: 0
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