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Yorodumi- PDB-7jr8: H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jr8 | ||||||
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Title | H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors | ||||||
Components | Hematopoietic prostaglandin D synthase | ||||||
Keywords | Isomerase / Transferase/Inhibitor / Hematopoietic prostaglandin D2 synthase / inhibitor / Transferase-Inhibitor complex | ||||||
Function / homology | Function and homology information prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior ...prostaglandin-D synthase / prostaglandin-D synthase activity / negative regulation of male germ cell proliferation / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Glutathione conjugation / prostaglandin biosynthetic process / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / locomotory behavior / intracellular membrane-bounded organelle / calcium ion binding / magnesium ion binding / signal transduction / protein homodimerization activity / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 Å | ||||||
Authors | Nolte, R.T. / Somers, D.O. / Gampe, R.T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2021 Title: A knowledge-based, structural-aided discovery of a novel class of 2-phenylimidazo[1,2-a]pyridine-6-carboxamide H-PGDS inhibitors. Authors: Schulte, C.A. / Deaton, D.N. / Diaz, E. / Do, Y. / Gampe, R.T. / Guss, J.H. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Holt, J. / Jeune, M.R. / Kahler, K.M. / Kramer, H.F. / Le, J. / ...Authors: Schulte, C.A. / Deaton, D.N. / Diaz, E. / Do, Y. / Gampe, R.T. / Guss, J.H. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Holt, J. / Jeune, M.R. / Kahler, K.M. / Kramer, H.F. / Le, J. / Mortenson, P.N. / Musetti, C. / Nolte, R.T. / Orband-Miller, L.A. / Peckham, G.E. / Petrov, K.G. / Pietrak, B.L. / Poole, C. / Price, D.J. / Saxty, G. / Shillings, A. / Smalley Jr., T.L. / Somers, D.O. / Stewart, E.L. / Stuart, J.D. / Thomson, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jr8.cif.gz | 356.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jr8.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jr8 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jr8 | 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23427.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Production host: Escherichia coli (E. coli) References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase |
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-Non-polymers , 7 types, 608 molecules
#2: Chemical | ChemComp-CL / | ||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein buffer 50mM TRIS pH 7.5 50mM NaCl ammneded with 15mM GSH, 5mM MgCl2, 5mM DTT, 1mM EDTA Well Buffer 20-32% PEG 6K, 1% 1,4 DIOXANE, 10mM DTT, 5% EG, 50mM TRIS pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→32.55 Å / Num. obs: 129853 / % possible obs: 84.58 % / Redundancy: 1.8 % / Biso Wilson estimate: 6.85 Å2 / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 13.11 |
Reflection shell | Resolution: 1.13→1.17 Å / Redundancy: 1.7 % / Num. unique obs: 7258 / CC1/2: 0.84 / CC star: 0.955 / % possible all: 49.01 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.13→32.55 Å / SU ML: 0.0629 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 12.6764 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→32.55 Å
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Refine LS restraints |
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LS refinement shell |
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