+Open data
-Basic information
Entry | Database: PDB / ID: 6viz | ||||||
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Title | BRD4_Bromodomain1 complex with pyrrolopyridone compound 27 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | SIGNALING PROTEIN / bromodomain | ||||||
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: 2.391 Å | ||||||
Authors | Longenecker, K.L. / Park, C.H. / Qiu, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery ofN-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with ...Title: Discovery ofN-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second Bromodomain. Authors: Sheppard, G.S. / Wang, L. / Fidanze, S.D. / Hasvold, L.A. / Liu, D. / Pratt, J.K. / Park, C.H. / Longenecker, K. / Qiu, W. / Torrent, M. / Kovar, P.J. / Bui, M. / Faivre, E. / Huang, X. / ...Authors: Sheppard, G.S. / Wang, L. / Fidanze, S.D. / Hasvold, L.A. / Liu, D. / Pratt, J.K. / Park, C.H. / Longenecker, K. / Qiu, W. / Torrent, M. / Kovar, P.J. / Bui, M. / Faivre, E. / Huang, X. / Lin, X. / Wilcox, D. / Zhang, L. / Shen, Y. / Albert, D.H. / Magoc, T.J. / Rajaraman, G. / Kati, W.M. / McDaniel, K.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6viz.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6viz.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 6viz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6viz_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 6viz_full_validation.pdf.gz | 484.3 KB | Display | |
Data in XML | 6viz_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 6viz_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6viz ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6viz | HTTPS FTP |
-Related structure data
Related structure data | 6viwC 6vixC 6viyC 5uvwS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13923.103 Da / Num. of mol.: 3 / Fragment: Bromodomain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.45 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2.0M Na Formate, 0.1M Bis-Tris Propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.391→122.482 Å / Num. obs: 31667 / % possible obs: 99.5 % / Redundancy: 19.5 % / Biso Wilson estimate: 67.69 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.391→2.432 Å / Redundancy: 19.9 % / Rmerge(I) obs: 1.582 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1552 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uvw Resolution: 2.391→122.48 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.159
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Displacement parameters | Biso max: 114.85 Å2 / Biso mean: 64.75 Å2 / Biso min: 38.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.391→122.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.391→2.41 Å / Rfactor Rfree error: 0
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