[English] 日本語
![](img/lk-miru.gif)
- PDB-5crm: Crystal Structure of the first bromodomain of human BRD4 in compl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5crm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand | ||||||
![]() | Bromodomain-containing protein 4 | ||||||
![]() | SIGNALING PROTEIN/INHIBITOR / BRD4 / Bromodomain / Four Alpha Helices / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Song, M. / Liu, Z. / Xue, X. / Xu, Y. | ||||||
![]() | ![]() Title: Discovery of Benzo[cd]indol-2(1H)-ones as Potent and Specific BET Bromodomain Inhibitors: Structure-Based Virtual Screening, Optimization, and Biological Evaluation Authors: Xue, X. / Zhang, Y. / Liu, Z. / Song, M. / Xing, Y. / Xiang, Q. / Wang, Z. / Tu, Z. / Zhou, Y. / Ding, K. / Xu, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 798.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 799 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5coiC ![]() 5cp5C ![]() 5cpeC ![]() 5cqtC ![]() 5crzC ![]() 5cs8C ![]() 5ctlC ![]() 5cy9C ![]() 5d0cC ![]() 5dx4C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16767.326 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-165 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 78 molecules ![](data/chem/img/NO3.gif)
![](data/chem/img/EB5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EB5.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EB5 / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-EDO / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.56 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.99→47.31 Å / Num. obs: 8601 / % possible obs: 92.9 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.022 / Net I/σ(I): 24.5 / Num. measured all: 50862 / Scaling rejects: 132 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 20.137 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→40.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|