+Open data
-Basic information
Entry | Database: PDB / ID: 5uey | ||||||
---|---|---|---|---|---|---|---|
Title | BRD4_BD2_A-1412838 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-88M / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.41 Å | ||||||
Authors | Park, C.H. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors. Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, ...Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, T.M. / Hubbard, R. / Park, C.H. / Li, L. / Magoc, T.J. / Albert, D.H. / Lin, X. / Warder, S.E. / Kovar, P. / Huang, X. / Wilcox, D. / Wang, R. / Rajaraman, G. / Petros, A.M. / Hutchins, C.W. / Panchal, S.C. / Sun, C. / Elmore, S.W. / Shen, Y. / Kati, W.M. / McDaniel, K.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uey.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uey.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 5uey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/5uey ftp://data.pdbj.org/pub/pdb/validation_reports/ue/5uey | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12806.933 Da / Num. of mol.: 1 / Fragment: residues 352-457 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O60885 |
---|---|
#2: Chemical | ChemComp-88M / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.63 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→33.4 Å / Num. obs: 5571 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 70 Å2 / Rsym value: 0.047 / Net I/σ(I): 18.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.41→33.38 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.85 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.504 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.302
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.16 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.41→33.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.41→2.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
|