[English] 日本語
Yorodumi- PDB-9fby: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with (5-(4-chloro-1-((tetrah... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fby | ||||||
---|---|---|---|---|---|---|---|
Title | N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with (5-(4-chloro-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | TRANSCRIPTION / BET / BROMODOMAIN / INHIBITOR / EPIGENETIC | ||||||
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 / Resolution: 1.853 Å | ||||||
Authors | Chung, C. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2024 Title: Structure- and Property-Based Optimization of Efficient Pan-Bromodomain and Extra Terminal Inhibitors to Identify Oral and Intravenous Candidate I-BET787. Authors: Hirst, D.J. / Bamborough, P. / Al-Mahdi, N. / Angell, D.C. / Barnett, H.A. / Baxter, A. / Bit, R.A. / Brown, J.A. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / Demont, E.H. / Ferrie, A. / ...Authors: Hirst, D.J. / Bamborough, P. / Al-Mahdi, N. / Angell, D.C. / Barnett, H.A. / Baxter, A. / Bit, R.A. / Brown, J.A. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / Demont, E.H. / Ferrie, A. / Gordon, L.J. / Harada, I. / Ho, T.C.T. / Holyer, I.D. / Hooper-Greenhill, E. / Jones, K.L. / Lindon, M.J. / Lovatt, C. / Lugo, D. / Maller, C. / McGonagle, G. / Messenger, C. / Mitchell, D.J. / Pascoe, D.D. / Patel, V.K. / Patten, C. / Poole, D.L. / Shah, R.R. / Rioja, I. / Stafford, K.A.J. / Tape, D. / Taylor, S. / Theodoulou, N.H. / Tomlinson, L. / Wall, I.D. / Wellaway, C.R. / White, G. / Prinjha, R.K. / Humphreys, P.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9fby.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9fby.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9fby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fby_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9fby_full_validation.pdf.gz | 810.7 KB | Display | |
Data in XML | 9fby_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 9fby_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/9fby ftp://data.pdbj.org/pub/pdb/validation_reports/fb/9fby | HTTPS FTP |
-Related structure data
Related structure data | 9fbxC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 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 | ChemComp-EDO / |
#3: Chemical | ChemComp-A1IB5 / Mass: 321.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20ClN3O2 / Feature type: SUBJECT OF INVESTIGATION |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.19 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MMT(Malic acid, MES, Tris) pH9.0,25% w/v PEG1500 PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→36.59 Å / Num. obs: 9882 / % possible obs: 98.5 % / Redundancy: 2.6 % / CC1/2: 0.969 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.85→2.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2285 / CC1/2: 0.649 / % possible all: 97.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.853→32.744 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.88 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.156 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.682 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.853→32.744 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|