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Yorodumi- PDB-7mls: X-ray crystal structure of human BRD4(D1) in complex with 2-(2,5-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mls | |||||||||
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Title | X-ray crystal structure of human BRD4(D1) in complex with 2-(2,5-dibromophenoxy)-6-[4-methyl-1-(piperidin-4-yl)-1H-1,2,3-triazol-5-yl]pyridine (compound 23) | |||||||||
Components | Bromodomain-containing protein 4 | |||||||||
Keywords | GENE REGULATION/INHIBITOR / BRD4 / GENE REGULATION / GENE REGULATION-INHIBITOR complex | |||||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.26 Å | |||||||||
Authors | Cui, H. / Johnson, J.A. / Zahid, H. / Buchholz, C.R. / Shi, K. / Aihara, H. / Pomerantz, W.C.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: 4-Methyl-1,2,3-Triazoles as N -Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. Authors: Cui, H. / Carlson, A.S. / Schleiff, M.A. / Divakaran, A. / Johnson, J.A. / Buchholz, C.R. / Zahid, H. / Vail, N.R. / Shi, K. / Aihara, H. / Harki, D.A. / Miller, G.P. / Topczewski, J.J. / Pomerantz, W.C.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mls.cif.gz | 112.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mls.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 7mls.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mls_validation.pdf.gz | 848.9 KB | Display | wwPDB validaton report |
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Full document | 7mls_full_validation.pdf.gz | 849.4 KB | Display | |
Data in XML | 7mls_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7mls_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7mls ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7mls | HTTPS FTP |
-Related structure data
Related structure data | 7mlqC 7mlrC 6wgxS S: Starting model for refinement 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60885 | ||||||
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#2: Chemical | ChemComp-ZHM / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.26→47.5 Å / Num. obs: 66134 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.09 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.022 / Rrim(I) all: 0.051 / Net I/σ(I): 23.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6WGX Resolution: 1.26→30.46 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 12.64 / 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: 59.87 Å2 / Biso mean: 14.4716 Å2 / Biso min: 3.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.26→30.46 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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