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Yorodumi- PDB-4yh3: Crystal structure of human BRD4(1) in complex with 4-[(2E)-3-(4-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yh3 | ||||||
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Title | Crystal structure of human BRD4(1) in complex with 4-[(2E)-3-(4-methoxyphenyl)-2-phenylprop-2-enoyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19a) | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | PROTEIN BINDING / BRD4(1) | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-Y80 / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | White, A. / Lakshminarasimhan, D. / Suto, R.K. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Discovery of a new chemical series of BRD4(1) inhibitors using protein-ligand docking and structure-guided design. Authors: Duffy, B.C. / Liu, S. / Martin, G.S. / Wang, R. / Hsia, M.M. / Zhao, H. / Guo, C. / Ellis, M. / Quinn, J.F. / Kharenko, O.A. / Norek, K. / Gesner, E.M. / Young, P.R. / McLure, K.G. / Wagner, ...Authors: Duffy, B.C. / Liu, S. / Martin, G.S. / Wang, R. / Hsia, M.M. / Zhao, H. / Guo, C. / Ellis, M. / Quinn, J.F. / Kharenko, O.A. / Norek, K. / Gesner, E.M. / Young, P.R. / McLure, K.G. / Wagner, G.S. / Lakshminarasimhan, D. / White, A. / Suto, R.K. / Hansen, H.C. / Kitchen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yh3.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yh3.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yh3_validation.pdf.gz | 747.4 KB | Display | wwPDB validaton report |
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Full document | 4yh3_full_validation.pdf.gz | 748.1 KB | Display | |
Data in XML | 4yh3_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 4yh3_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yh3 ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yh3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15329.598 Da / Num. of mol.: 1 / Fragment: Bromodomain 1 (UNP residues 44-170) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pJExpress401 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-Y80 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG3350, 0.1 M HEPES, pH 7.5, 0.2 M L-proline, soaked in 20 mM ligand for 3 hours at room temperature |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 17723 / % possible obs: 98.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Χ2: 1.49 / Net I/av σ(I): 24.092 / Net I/σ(I): 11.7 / Num. measured all: 106654 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.24 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.875 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.093 / 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: 84.12 Å2 / Biso mean: 29.6066 Å2 / Biso min: 18.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.598→1.639 Å / Total num. of bins used: 20
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