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- PDB-5i83: Crystal structure of the bromodomain of human CREBBP bound to the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i83 | ||||||
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Title | Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepinone G02773986 | ||||||
![]() | CREB-binding protein![]() | ||||||
![]() | PROTEIN BINDING/INHIBITOR / ![]() | ||||||
Function / homology | ![]() peptide lactyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jayaram, H. / Poy, F. / Setser, J.W. / Bellon, S.F. | ||||||
![]() | ![]() Title: Fragment-Based Discovery of a Selective and Cell-Active Benzodiazepinone CBP/EP300 Bromodomain Inhibitor (CPI-637). Authors: Taylor, A.M. / Cote, A. / Hewitt, M.C. / Pastor, R. / Leblanc, Y. / Nasveschuk, C.G. / Romero, F.A. / Crawford, T.D. / Cantone, N. / Jayaram, H. / Setser, J. / Murray, J. / Beresini, M.H. / ...Authors: Taylor, A.M. / Cote, A. / Hewitt, M.C. / Pastor, R. / Leblanc, Y. / Nasveschuk, C.G. / Romero, F.A. / Crawford, T.D. / Cantone, N. / Jayaram, H. / Setser, J. / Murray, J. / Beresini, M.H. / de Leon Boenig, G. / Chen, Z. / Conery, A.R. / Cummings, R.T. / Dakin, L.A. / Flynn, E.M. / Huang, O.W. / Kaufman, S. / Keller, P.J. / Kiefer, J.R. / Lai, T. / Li, Y. / Liao, J. / Liu, W. / Lu, H. / Pardo, E. / Tsui, V. / Wang, J. / Wang, Y. / Xu, Z. / Yan, F. / Yu, D. / Zawadzke, L. / Zhu, X. / Zhu, X. / Sims, R.J. / Cochran, A.G. / Bellon, S. / Audia, J.E. / Magnuson, S. / Albrecht, B.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 | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i86C ![]() 5i89C ![]() 5i8bC ![]() 5i8gC ![]() 3dwyS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | ![]() Mass: 13992.011 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 1082-1197) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SCN / ![]() |
#3: Chemical | ChemComp-68Y / ( |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 9, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→50 Å / Num. obs: 30903 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Χ2: 1.049 / Net I/av σ(I): 17.412 / Net I/σ(I): 10.2 / Num. measured all: 175849 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3DWY Resolution: 1.35→31.58 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.151 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.48 Å2 / Biso mean: 20.686 Å2 / Biso min: 9.76 Å2
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Refinement step | Cycle: final / Resolution: 1.35→31.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.355→1.39 Å / Total num. of bins used: 20
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