[English] 日本語
Yorodumi- PDB-8wy7: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wy7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 22 | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | PROTEIN BINDING / BRD4(1) / Bromodomain | ||||||
Function / homology | Amanitin/phalloidin toxin / toxin activity / Chem-XHN / Alpha-amanitin proprotein 1 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Xu, H. / Zhao, X. / Shen, H. / Xu, Y. / Wu, X. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2024 Title: Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia. Authors: Jiang, W. / Hou, Q. / Xu, H. / Yang, K. / Wang, X. / Zhang, K. / Zeng, Y. / Li, W. / Wang, B. / Luo, G. / Zhao, X. / Shen, H. / Xu, Y. / Wu, X. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8wy7.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8wy7.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wy7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8wy7_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8wy7_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 8wy7_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/8wy7 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/8wy7 | HTTPS FTP |
-Related structure data
Related structure data | 8wxyC 8wy3C 8wygC 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: 16767.326 Da / Num. of mol.: 3 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 / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.5 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0 M Sodium formate, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→134.3 Å / Num. obs: 18153 / % possible obs: 94.7 % / Redundancy: 17.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.052 / Rrim(I) all: 0.214 / Net I/σ(I): 20 / Num. measured all: 317495 |
Reflection shell | Resolution: 2.83→2.98 Å / % possible obs: 100 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.949 / Num. measured all: 56702 / Num. unique obs: 2736 / CC1/2: 0.803 / Rpim(I) all: 0.204 / Rrim(I) all: 0.971 / Net I/σ(I) obs: 2.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→121.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.414 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.464 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.83→121.37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|