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- PDB-7rxs: Crystal of BRD4(D1) with 2-[(3S)-3-{5-[2-(3,5-dimethylphenoxy)pyr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rxs | |||||||||
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Title | Crystal of BRD4(D1) with 2-[(3S)-3-{5-[2-(3,5-dimethylphenoxy)pyrimidin-4-yl]-4-(4-iodophenyl)-1H-imidazol-1-yl}pyrrolidin-1-yl]ethan-1-amine | |||||||||
![]() | Bromodomain-containing protein 4 | |||||||||
![]() | GENE REGULATION/INHIBITOR / BRD4 / GENE REGULATION / GENE REGULATION-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 | ![]() ![]() ![]() | |||||||||
![]() | Cui, H. / Johnson, J.A. / Shi, K. / Aihara, H. / Pomerantz, W.C.K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. Authors: Cui, H. / Divakaran, A. / Hoell, Z.J. / Ellingson, M.O. / Scholtz, C.R. / Zahid, H. / Johnson, J.A. / Griffith, E.C. / Gee, C.T. / Lee, A.L. / Khanal, S. / Shi, K. / Aihara, H. / Shah, V.H. ...Authors: Cui, H. / Divakaran, A. / Hoell, Z.J. / Ellingson, M.O. / Scholtz, C.R. / Zahid, H. / Johnson, J.A. / Griffith, E.C. / Gee, C.T. / Lee, A.L. / Khanal, S. / Shi, K. / Aihara, H. / Shah, V.H. / Lee, R.E. / Harki, D.A. / Pomerantz, W.C.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800.5 KB | Display | ![]() |
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Full document | ![]() | 801.8 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r9cC ![]() 7rxrC ![]() 7rxtC ![]() 7jt4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-7ZT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.43→41.45 Å / Num. obs: 25500 / % possible obs: 97.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Net I/σ(I): 16.1 / Num. measured all: 123698 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7jt4 Resolution: 1.43→38.79 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.07 Å2 / Biso mean: 29.9744 Å2 / Biso min: 12.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.43→38.79 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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