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Yorodumi- PDB-4meo: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4meo | ||||||
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Title | Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-methyl-quinoline ligand | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION/TRANSCRIPTION inhibitor / BRD4 / CAP / HUNK1 / MCAP / Mitotic chromosome associated protein / BRD / Small molecule inhibitor / Structural Genomics COnsortium / SGC / TRANSCRIPTION-TRANSCRIPTION inhibitor complex | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Fedorov, O. / Vidler, L.R. / Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Filippakopoulos, P. / Picaud, S. / Felletar, I. / Martin, S. / Fedorov, O. / Vidler, L.R. / Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Hoelder, S. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Discovery of Novel Small-Molecule Inhibitors of BRD4 Using Structure-Based Virtual Screening. Authors: Vidler, L.R. / Filippakopoulos, P. / Fedorov, O. / Picaud, S. / Martin, S. / Tomsett, M. / Woodward, H. / Brown, N. / Knapp, S. / Hoelder, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4meo.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4meo.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 4meo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4meo ftp://data.pdbj.org/pub/pdb/validation_reports/me/4meo | HTTPS FTP |
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-Related structure data
Related structure data | 4menC 4mepC 4meqC 2ossS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 15099.380 Da / Num. of mol.: 1 / Fragment: unp residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: O60885 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-25V / |
#4: Chemical | ChemComp-DMS / |
#5: 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: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.20M LiCl, 0.1M TRIS, 20.0% PEG 6K, 10.0% EtGly, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 17, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 4.4 % / Av σ(I) over netI: 6.6 / Number: 64294 / Rsym value: 0.101 / D res high: 1.715 Å / D res low: 29.24 Å / Num. obs: 14452 / % possible obs: 99.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.72→29.24 Å / Num. all: 14481 / Num. obs: 14452 / % possible obs: 99.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.72→29.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1959 / WRfactor Rwork: 0.1512 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.894 / SU B: 3.815 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1128 / SU Rfree: 0.1149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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: 89.89 Å2 / Biso mean: 17.0564 Å2 / Biso min: 6.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.715→1.759 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 30.8017 Å / Origin y: 25.7695 Å / Origin z: 8.7758 Å
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