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Yorodumi- PDB-5bqh: Discovery of a Potent and Selective mPGES-1 Inhibitor for the Tre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bqh | ||||||
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Title | Discovery of a Potent and Selective mPGES-1 Inhibitor for the Treatment of Pain | ||||||
Components | Prostaglandin E synthase | ||||||
Keywords | Isomerase/isomerase inhibitor / mPGES-1 / enzyme / integral membrane protein / 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 / prostaglandin metabolic process ...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 / prostaglandin metabolic process / nuclear envelope lumen / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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: 1.601 Å | ||||||
Authors | Fisher, M.J. / Schiffler, M.A. / Kuklish, S.L. / Antonysamy, S. / Luz, J.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery and Characterization of 2-Acylaminoimidazole Microsomal Prostaglandin E Synthase-1 Inhibitors. Authors: Schiffler, M.A. / Antonysamy, S. / Bhattachar, S.N. / Campanale, K.M. / Chandrasekhar, S. / Condon, B. / Desai, P.V. / Fisher, M.J. / Groshong, C. / Harvey, A. / Hickey, M.J. / Hughes, N.E. ...Authors: Schiffler, M.A. / Antonysamy, S. / Bhattachar, S.N. / Campanale, K.M. / Chandrasekhar, S. / Condon, B. / Desai, P.V. / Fisher, M.J. / Groshong, C. / Harvey, A. / Hickey, M.J. / Hughes, N.E. / Jones, S.A. / Kim, E.J. / Kuklish, S.L. / Luz, J.G. / Norman, B.H. / Rathmell, R.E. / Rizzo, J.R. / Seng, T.W. / Thibodeaux, S.J. / Woods, T.A. / York, J.S. / Yu, X.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bqh.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bqh.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 5bqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/5bqh ftp://data.pdbj.org/pub/pdb/validation_reports/bq/5bqh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 17307.559 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 |
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#4: Sugar |
-Non-polymers , 5 types, 127 molecules
#2: Chemical | ChemComp-4UK / |
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#3: Chemical | ChemComp-GSH / |
#5: Chemical | ChemComp-PG4 / |
#6: Chemical | ChemComp-1KA / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.43 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris HCl pH 9.2 + 32% PEG 1K |
-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 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: 1.6→30 Å / Num. obs: 33609 / % possible obs: 99.6 % / Redundancy: 5.6 % / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
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Refinement | Resolution: 1.601→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.22 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.692 Å2
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Refinement step | Cycle: 1 / Resolution: 1.601→30 Å
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Refine LS restraints |
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