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- PDB-4w2r: Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w2r | ||||||
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Title | Structure of Hs/AcPRC2 in complex with 5,8-dichloro-2-[(4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-[(R)-methoxy(oxetan-3-yl)methyl]-3,4-dihydroisoquinolin-1(2H)-one | ||||||
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![]() | Transferase/Transferase Inhibitor / LYSINE METHYLTRANSFERASE / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | ![]() [histone H3]-lysine27 N-trimethyltransferase / sex chromatin / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / facultative heterochromatin formation / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / lncRNA binding / spinal cord development ...[histone H3]-lysine27 N-trimethyltransferase / sex chromatin / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / facultative heterochromatin formation / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / lncRNA binding / spinal cord development / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / negative regulation of cell differentiation / heterochromatin formation / nucleosome binding / enzyme activator activity / methylated histone binding / SUMOylation of chromatin organization proteins / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / promoter-specific chromatin binding / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / rhythmic process / chromosome / methylation / Oxidative Stress Induced Senescence / cell population proliferation / nuclear body / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
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![]() | Gajiwala, K.S. / Brooun, A. / Liu, W. / Deng, Y. / Stewart, A.E. | ||||||
![]() | ![]() Title: Optimization of Orally Bioavailable Enhancer of Zeste Homolog 2 (EZH2) Inhibitors Using Ligand and Property-Based Design Strategies: Identification of Development Candidate (R)-5,8-Dichloro-7- ...Title: Optimization of Orally Bioavailable Enhancer of Zeste Homolog 2 (EZH2) Inhibitors Using Ligand and Property-Based Design Strategies: Identification of Development Candidate (R)-5,8-Dichloro-7-(methoxy(oxetan-3-yl)methyl)-2-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-3,4-dihydroisoquinolin-1(2H)-one (PF-06821497). Authors: Kung, P.P. / Bingham, P. / Brooun, A. / Collins, M. / Deng, Y.L. / Dinh, D. / Fan, C. / Gajiwala, K.S. / Grantner, R. / Gukasyan, H.J. / Hu, W. / Huang, B. / Kania, R. / Kephart, S.E. / ...Authors: Kung, P.P. / Bingham, P. / Brooun, A. / Collins, M. / Deng, Y.L. / Dinh, D. / Fan, C. / Gajiwala, K.S. / Grantner, R. / Gukasyan, H.J. / Hu, W. / Huang, B. / Kania, R. / Kephart, S.E. / Krivacic, C. / Kumpf, R.A. / Khamphavong, P. / Kraus, M. / Liu, W. / Maegley, K.A. / Nguyen, L. / Ren, S. / Richter, D. / Rollins, R.A. / Sach, N. / Sharma, S. / Sherrill, J. / Spangler, J. / Stewart, A.E. / Sutton, S. / Uryu, S. / Verhelle, D. / Wang, H. / Wang, S. / Wythes, M. / Xin, S. / Yamazaki, S. / Zhu, H. / Zhu, J. / Zehnder, L. / Edwards, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 399.5 KB | Display | ![]() |
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PDB format | ![]() | 320.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 73.8 KB | Display | |
Data in CIF | ![]() | 98.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6b3wC ![]() 5ij7S 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
#1: Protein | Mass: 72941.484 Da / Num. of mol.: 2 / Fragment: UNP residues 4-332, 420-478, 502-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 41776.535 Da / Num. of mol.: 2 / Fragment: UNP residues 81-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 22268.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-ZN / #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: Precipitant: 26.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.70) |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→148.01 Å / Num. obs: 58162 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 68.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.81→3.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.2 / Num. unique all: 16475 / CC1/2: 0.907 / Rpim(I) all: 0.246 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5IJ7 Resolution: 2.81→148.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1424624 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0754 Å2 / ksol: 0.3516 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.15 Å2 / Biso mean: 72.4 Å2 / Biso min: 35.29 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 2.81→148.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.99 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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