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- PDB-7jr8: H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxam... -

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Basic information

Entry
Database: PDB / ID: 7jr8
TitleH-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxamide inhibitors
ComponentsHematopoietic prostaglandin D synthase
KeywordsIsomerase / 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
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Chem-VH7 / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 Å
AuthorsNolte, R.T. / Somers, D.O. / Gampe, R.T.
CitationJournal: 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
DepositionAug 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hematopoietic prostaglandin D synthase
B: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,56515
Polymers46,8562
Non-polymers1,70913
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-75 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.082, 93.489, 47.913
Angle α, β, γ (deg.)90.000, 105.519, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hematopoietic prostaglandin D synthase / H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / ...H-PGDS / GST class-sigma / Glutathione S-transferase / Glutathione-dependent PGD synthase / Glutathione-requiring prostaglandin D synthase / Prostaglandin-H2 D-isomerase


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 / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Chemical ChemComp-VH7 / N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-2-phenylimidazo[1,2-a]pyridine-6-carboxamide


Mass: 377.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27N3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.13→1.17 Å / Redundancy: 1.7 % / Num. unique obs: 7258 / CC1/2: 0.84 / CC star: 0.955 / % possible all: 49.01

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1433 1792 1.42 %
Rwork0.1148 124047 -
obs0.1152 125839 84.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.9 Å2
Refinement stepCycle: LAST / Resolution: 1.13→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 114 595 4004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00933776
X-RAY DIFFRACTIONf_angle_d1.13115173
X-RAY DIFFRACTIONf_chiral_restr0.0835551
X-RAY DIFFRACTIONf_plane_restr0.0101670
X-RAY DIFFRACTIONf_dihedral_angle_d19.32531433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.160.198910.18145101X-RAY DIFFRACTION45.78
1.16-1.190.19531250.15738071X-RAY DIFFRACTION71.47
1.19-1.230.19251290.14219468X-RAY DIFFRACTION84.05
1.23-1.280.15321380.12519691X-RAY DIFFRACTION85.92
1.28-1.330.14241230.11479779X-RAY DIFFRACTION87.07
1.33-1.390.14111530.105910026X-RAY DIFFRACTION89.06
1.39-1.460.14251540.099510159X-RAY DIFFRACTION90.13
1.46-1.550.12291550.092310381X-RAY DIFFRACTION92.1
1.55-1.670.13221640.09210498X-RAY DIFFRACTION93.13
1.67-1.840.12491530.098410643X-RAY DIFFRACTION94.25
1.84-2.110.12811630.101210810X-RAY DIFFRACTION95.81
2.11-2.660.13421030.11088223X-RAY DIFFRACTION72.55
2.66-32.550.14941410.128611197X-RAY DIFFRACTION97.78

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