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- PDB-4yc9: Crystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yc9 | ||||||
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Title | Crystal structure of TRIM24 PHD-bromodomain complexed with N-(6-{3-[4-(dimethylamino)butoxy]-5-propoxyphenoxy}-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl)-3,4-dimethoxybenzene-1-sulfonamide (8i) | ||||||
![]() | Transcription intermediary factor 1-alpha | ||||||
![]() | TRANSCRIPTION/TRANSCRIPTION INHIBITOR / Center for Biomolecular Structure and Function / Bromodomain / TRIM24 / inhibitor / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex | ||||||
Function / homology | ![]() perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / male germ cell nucleus ...perichromatin fibrils / regulation of vitamin D receptor signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / cellular response to estrogen stimulus / estrogen response element binding / calcium ion homeostasis / Signaling by FGFR1 in disease / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / male germ cell nucleus / nuclear receptor binding / lysine-acetylated histone binding / RING-type E3 ubiquitin transferase / regulation of protein stability / euchromatin / protein catabolic process / response to peptide hormone / negative regulation of epithelial cell proliferation / ubiquitin protein ligase activity / Signaling by BRAF and RAF1 fusions / p53 binding / regulation of apoptotic process / transcription by RNA polymerase II / transcription coactivator activity / protein kinase activity / protein ubiquitination / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / chromatin / mitochondrion / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Poncet-Montange, G. / Palmer, W. / Jones, P. | ||||||
![]() | ![]() Title: Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor. Authors: Palmer, W.S. / Poncet-Montange, G. / Liu, G. / Petrocchi, A. / Reyna, N. / Subramanian, G. / Theroff, J. / Yau, A. / Kost-Alimova, M. / Bardenhagen, J.P. / Leo, E. / Shepard, H.E. / Tieu, T. ...Authors: Palmer, W.S. / Poncet-Montange, G. / Liu, G. / Petrocchi, A. / Reyna, N. / Subramanian, G. / Theroff, J. / Yau, A. / Kost-Alimova, M. / Bardenhagen, J.P. / Leo, E. / Shepard, H.E. / Tieu, T.N. / Shi, X. / Zhan, Y. / Zhao, S. / Barton, M.C. / Draetta, G. / Toniatti, C. / Jones, P. / Geck Do, M. / Andersen, J.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yabC ![]() 4yadC ![]() 4yatC ![]() 4yaxC ![]() 4ybmC ![]() 4ybsC ![]() 4ybtC ![]() 3o34S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21318.395 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 824-1006) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O15164, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-4C1 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→60.576 Å / Num. all: 17452 / Num. obs: 17452 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.111 / Rsym value: 0.088 / Net I/av σ(I): 5.565 / Net I/σ(I): 7 / Num. measured all: 66226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3O34 Resolution: 1.82→42.58 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.286 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 115.41 Å2 / Biso mean: 36.339 Å2 / Biso min: 19.4 Å2
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Refinement step | Cycle: final / Resolution: 1.82→42.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Total num. of bins used: 20
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