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Yorodumi- PDB-6vub: Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vub | ||||||
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Title | Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 5 (1-methyl-4-phenylpyrrolidin-2-one) | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | PROTEIN BINDING / BRD4 BD1 / Bromodomain / NMP | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ilyichova, O.V. / Scanlon, M.J. / Thompson, P.E. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2020 Title: Substituted 1-methyl-4-phenylpyrrolidin-2-ones - Fragment-based design of N-methylpyrrolidone-derived bromodomain inhibitors. Authors: Hilton-Proctor, J.P. / Ilyichova, O. / Zheng, Z. / Jennings, I.G. / Johnstone, R.W. / Shortt, J. / Mountford, S.J. / Scanlon, M.J. / Thompson, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vub.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vub.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vub_validation.pdf.gz | 313 KB | Display | wwPDB validaton report |
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Full document | 6vub_full_validation.pdf.gz | 313 KB | Display | |
Data in XML | 6vub_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6vub_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/6vub ftp://data.pdbj.org/pub/pdb/validation_reports/vu/6vub | HTTPS FTP |
-Related structure data
Related structure data | 6vucC 6vufC 6vujC 5dw2S 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: 14968.182 Da / Num. of mol.: 1 / Fragment: bromodomain 1 (UNP residues 44-168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28(a) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O60885 |
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#2: Chemical | ChemComp-RLG / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 5, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.24 Å / Num. obs: 21587 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 7.59 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.097 / Rrim(I) all: 0.202 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1063 / CC1/2: 0.828 / Rpim(I) all: 0.583 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5DW2 Resolution: 1.5→39.24 Å / SU ML: 0.1197 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.124
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.24 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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