+Open data
-Basic information
Entry | Database: PDB / ID: 6vix | ||||||
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Title | BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | SIGNALING PROTEIN / bromodomain | ||||||
Function / homology | Amanitin/phalloidin toxin / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / toxin activity / Up-down Bundle / Mainly Alpha / Chem-QYV / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.116 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 | 6vix.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vix.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vix_validation.pdf.gz | 560.6 KB | Display | wwPDB validaton report |
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Full document | 6vix_full_validation.pdf.gz | 563.3 KB | Display | |
Data in XML | 6vix_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6vix_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6vix ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vix | HTTPS FTP |
-Related structure data
Related structure data | 6viwC 6viyC 6vizC 5uvsS 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12863.983 Da / Num. of mol.: 4 / Fragment: Bromodomain 2 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 | ChemComp-QYV / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.83 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 25% PEG 3350, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5 |
-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: Oct 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.116→82.94 Å / Num. obs: 30976 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 39.18 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.116→2.153 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 1438 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5uvs Resolution: 2.116→82.94 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.175
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Displacement parameters | Biso max: 92.59 Å2 / Biso mean: 38.61 Å2 / Biso min: 21.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.116→82.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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