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- PDB-7l50: Crystal structure of human monoacylglycerol lipase in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l50 | ||||||
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Title | Crystal structure of human monoacylglycerol lipase in complex with compound 4f | ||||||
![]() | Monoglyceride lipase | ||||||
![]() | HYDROLASE/INHIBITOR / Inhibitor / Serine hydrolase / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() acylglycerol metabolic process / monoacylglycerol lipase activity / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, L. / Lane, W. / Skene, R.J. | ||||||
![]() | ![]() Title: Design and Synthesis of Novel Spiro Derivatives as Potent and Reversible Monoacylglycerol Lipase (MAGL) Inhibitors: Bioisosteric Transformation from 3-Oxo-3,4-dihydro-2 H -benzo[ b ][1,4]oxazin-6-yl Moiety. Authors: Ikeda, S. / Sugiyama, H. / Tokuhara, H. / Murakami, M. / Nakamura, M. / Oguro, Y. / Aida, J. / Morishita, N. / Sogabe, S. / Dougan, D.R. / Gay, S.C. / Qin, L. / Arimura, N. / Takahashi, Y. / ...Authors: Ikeda, S. / Sugiyama, H. / Tokuhara, H. / Murakami, M. / Nakamura, M. / Oguro, Y. / Aida, J. / Morishita, N. / Sogabe, S. / Dougan, D.R. / Gay, S.C. / Qin, L. / Arimura, N. / Takahashi, Y. / Sasaki, M. / Kamada, Y. / Aoyama, K. / Kimoto, K. / Kamata, 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 | ![]() | 430.5 KB | Display | ![]() |
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PDB format | ![]() | 346 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 44.1 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l4tC ![]() 7l4uC ![]() 7l4wC ![]() 5zunS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35234.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-XOM / ( #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaOAc pH 5.5, 32-38% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→49.06 Å / Num. obs: 79270 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.072 / Rrim(I) all: 0.143 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.728 / Num. unique obs: 4493 / CC1/2: 0.868 / Rpim(I) all: 0.439 / Rrim(I) all: 0.854 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ZUN Resolution: 2.3→48.191 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 31.945 / SU ML: 0.304 / Cross valid method: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.222 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.191 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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