+Open data
-Basic information
Entry | Database: PDB / ID: 5k0i | ||||||
---|---|---|---|---|---|---|---|
Title | mpges1 bound to an inhibitor | ||||||
Components | Prostaglandin E synthase | ||||||
Keywords | Isomerase/Isomerase Inhibitor / mpges1 / inhibitor / pain / inflammation / Isomerase-Isomerase Inhibitor complex | ||||||
Function / homology | Function and homology information regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases ...regulation of fever generation / prostaglandin-E synthase / prostaglandin-E synthase activity / prostaglandin-D synthase activity / positive regulation of prostaglandin secretion / glutathione binding / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / glutathione peroxidase activity / prostaglandin biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / sensory perception of pain / regulation of inflammatory response / cell population proliferation / negative regulation of cell population proliferation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / signal transduction / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å | ||||||
Authors | Luz, J.G. / Kuklish, S.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2016 Title: Characterization of 3,3-dimethyl substituted N-aryl piperidines as potent microsomal prostaglandin E synthase-1 inhibitors. Authors: Kuklish, S.L. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A.J. / Gooding, K. / Harvey, A. / Hughes, N.E. / Luz, J.G. / Manninen, P.R. / McGee, J.E. / ...Authors: Kuklish, S.L. / Antonysamy, S. / Bhattachar, S.N. / Chandrasekhar, S. / Fisher, M.J. / Fretland, A.J. / Gooding, K. / Harvey, A. / Hughes, N.E. / Luz, J.G. / Manninen, P.R. / McGee, J.E. / Navarro, A. / Norman, B.H. / Partridge, K.M. / Quimby, S.J. / Schiffler, M.A. / Sloan, A.V. / Warshawsky, A.M. / York, J.S. / Yu, X.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5k0i.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5k0i.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/5k0i ftp://data.pdbj.org/pub/pdb/validation_reports/k0/5k0i | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 17323.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTGES, MGST1L1, MPGES1, PGES, PIG12 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14684, prostaglandin-E synthase |
---|---|
#4: Sugar |
-Non-polymers , 4 types, 137 molecules
#2: Chemical | ChemComp-6PW / | ||
---|---|---|---|
#3: Chemical | ChemComp-GSH / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.12 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M tris pH 9.4, 36% PEG 1K |
-Data collection
Diffraction | Mean temperature: 78 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Aug 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→19.65 Å / Num. obs: 74628 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 6.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.3→19.65 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.963 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.208 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→19.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|