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Yorodumi- PDB-7ymg: Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 2-(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ymg | |||||||||
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Title | Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 2-({3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}amino)-3-(1H-indol-3-yl)propan-1-ol | |||||||||
Components | Bromodomain-containing protein 4 | |||||||||
Keywords | TRANSCRIPTION / BRD4 / BET 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Kim, J.H. / Lee, B.I. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Sci Rep / Year: 2023 Title: Crystal structure of [1,2,4]triazolo[4,3-b]pyridazine derivatives as BRD4 bromodomain inhibitors and structure-activity relationship study. Authors: Kim, J.H. / Pandit, N. / Yoo, M. / Park, T.H. / Choi, J.U. / Park, C.H. / Jung, K.Y. / Lee, B.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ymg.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ymg.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ymg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ymg ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ymg | HTTPS FTP |
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-Related structure data
Related structure data | 7yq9C 8gpzC 8gq0C 6kekS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15025.235 Da / Num. of mol.: 2 / Fragment: bromodomain 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pHis / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885 |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.87 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Protein concentration 12 mg/mL Protein Stoarage buffer: 10mM HEPES pH 7.5, 500mM NaCl, 5% Glycerol, 10 mM DTT Reservoir solution: 5M sodium formate, 6% glycerol (Protein/reservoir= ...Details: Protein concentration 12 mg/mL Protein Stoarage buffer: 10mM HEPES pH 7.5, 500mM NaCl, 5% Glycerol, 10 mM DTT Reservoir solution: 5M sodium formate, 6% glycerol (Protein/reservoir= 1000nL/1000nL) co-crystallization: added 5 mM chemical and incubated overnight at 4 celsius. PH range: 7.0~8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 51025 / % possible obs: 99.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 12.56 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.033 / Rrim(I) all: 0.073 / Rsym value: 0.052 / Χ2: 0.938 / Net I/σ(I): 24.878 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2526 / CC1/2: 0.708 / CC star: 0.911 / Rpim(I) all: 0.442 / Rrim(I) all: 0.971 / Rsym value: 0.723 / Χ2: 0.795 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KEK Resolution: 1.4→30.54 Å / SU ML: 0.1192 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4358 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30.54 Å
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Refine LS restraints |
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LS refinement shell |
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