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- PDB-5u69: Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u69 | ||||||
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Title | Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine | ||||||
![]() | Polycomb protein EED | ||||||
![]() | PROTEIN BINDING / INHIBITOR / WD40 PRC2 | ||||||
Function / homology | ![]() ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / nucleosome binding / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / nucleosome binding / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / chromosome / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jakob, C.G. / Zhu, H. | ||||||
![]() | ![]() Title: SAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding. Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / ...Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / Algire, M.A. / He, Y. / Richardson, P.L. / Sweis, R.F. / Sun, C. / Chiang, G.G. / Michaelides, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.6 KB | Display | ![]() |
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PDB format | ![]() | 141 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 808.4 KB | Display | ![]() |
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Full document | ![]() | 808.4 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u6dC ![]() 5u8aC ![]() 5u8fC ![]() 5k0mS 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: 42583.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LQD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 8.5 Details: 3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→62.58 Å / Num. obs: 118159 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.28→1.33 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5K0M Resolution: 1.28→62.58 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.198 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.035 / 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 mean: 16.733 Å2
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Refinement step | Cycle: 1 / Resolution: 1.28→62.58 Å
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Refine LS restraints |
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