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Yorodumi- PDB-4uiz: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uiz | ||||||
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Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-2-(4-methanesulfonylpiperazine-1-carbonyl)-5-methyl-4H,5H-thieno-3,2-c- pyridin-4-one | ||||||
Components | BROMODOMAIN-CONTAINING PROTEIN 4 | ||||||
Keywords | TRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST | ||||||
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 / chromatin / 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: 1.19 Å | ||||||
Authors | Chung, C. / Theodoulou, N.T. / Bamborough, P. / Humphreys, P.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: The Discovery of I-Brd9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / ...Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Michon, A. / Molnar, J. / Robson, S.C. / Tomkinson, N.C.O. / Kouzarides, T. / Prinjha, R.K. / Humphreys, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uiz.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uiz.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uiz_validation.pdf.gz | 753 KB | Display | wwPDB validaton report |
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Full document | 4uiz_full_validation.pdf.gz | 754 KB | Display | |
Data in XML | 4uiz_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 4uiz_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uiz ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uiz | HTTPS FTP |
-Related structure data
Related structure data | 4uitC 4uiuC 4uivC 4uiwC 4uixC 4uiyC 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: N-TERMINAL BROMODOMAIN, RESIDUES 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET26B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885 | ||||
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#2: Chemical | #3: Chemical | ChemComp-N1D / | #4: 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: 2.17 Å3/Da / Density % sol: 43.31 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1M BTP PH 6.5, 20% PEG3350, 0.2M NAFORMATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Jan 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→38.77 Å / Num. obs: 41778 / % possible obs: 1.2 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.19→1.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.1 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→38.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.941 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.634 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→38.77 Å
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