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- PDB-6n4e: hPGDS complexed with a quinoline-3-carboxamide -

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Basic information

Entry
Database: PDB / ID: 6n4e
TitlehPGDS complexed with a quinoline-3-carboxamide
ComponentsHematopoietic prostaglandin D synthase
KeywordsHYDROLASE
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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Chem-KCD / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShewchuk, L.M. / Ward, P.
CitationJournal: Bioorg. Med. Chem. / Year: 2019
Title: The discovery of quinoline-3-carboxamides as hematopoietic prostaglandin D synthase (H-PGDS) inhibitors.
Authors: Deaton, D.N. / Do, Y. / Holt, J. / Jeune, M.R. / Kramer, H.F. / Larkin, A.L. / Orband-Miller, L.A. / Peckham, G.E. / Poole, C. / Price, D.J. / Schaller, L.T. / Shen, Y. / Shewchuk, L.M. / ...Authors: Deaton, D.N. / Do, Y. / Holt, J. / Jeune, M.R. / Kramer, H.F. / Larkin, A.L. / Orband-Miller, L.A. / Peckham, G.E. / Poole, C. / Price, D.J. / Schaller, L.T. / Shen, Y. / Shewchuk, L.M. / Stewart, E.L. / Stuart, J.D. / Thomson, S.A. / Ward, P. / Wilson, J.W. / Xu, T. / Guss, J.H. / Musetti, C. / Rendina, A.R. / Affleck, K. / Anders, D. / Hancock, A.P. / Hobbs, H. / Hodgson, S.T. / Hutchinson, J. / Leveridge, M.V. / Nicholls, H. / Smith, I.E.D. / Somers, D.O. / Sneddon, H.F. / Uddin, S. / Cleasby, A. / Mortenson, P.N. / Richardson, C. / Saxty, G.
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
A: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1143
Polymers23,4281
Non-polymers6862
Water2,594144
1
A: Hematopoietic prostaglandin D synthase
hetero molecules

A: Hematopoietic prostaglandin D synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2276
Polymers46,8562
Non-polymers1,3714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4030 Å2
ΔGint-29 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.599, 72.760, 93.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPGDS, GSTS, PGDS, PTGDS2 / Plasmid: pET24 / Production host: Escherichia coli (E. coli)
References: UniProt: O60760, prostaglandin-D synthase, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-KCD / 7-(difluoromethoxy)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]quinoline-3-carboxamide


Mass: 378.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24F2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% Peg6K, 0.05 M tris pH 8.5, 5% glycerol, 10 mM DTT, 1% 1,4 Dioxane

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 26009 / % possible obs: 94.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6 % / Rmerge(I) obs: 0.637 / Num. unique obs: 1052 / % possible all: 77.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.72 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.337 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1025 4.7 %RANDOM
Rwork0.1931 ---
obs0.1937 20793 79.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.69 Å2 / Biso mean: 18.307 Å2 / Biso min: 4.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.09 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.65→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 47 144 1821
Biso mean--16.54 20.31 -
Num. residues----199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191733
X-RAY DIFFRACTIONr_bond_other_d0.0020.021582
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9812363
X-RAY DIFFRACTIONr_angle_other_deg0.95233667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8915202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36824.07481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88915288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5351510
X-RAY DIFFRACTIONr_chiral_restr0.070.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211889
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
LS refinement shellResolution: 1.648→1.691 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 56 -
Rwork0.224 962 -
all-1018 -
obs--50.3 %
Refinement TLS params.Method: refined / Origin x: 3.814 Å / Origin y: 18.45 Å / Origin z: -11.873 Å
111213212223313233
T0.0045 Å2-0.0121 Å2-0.0039 Å2-0.0472 Å20.0201 Å2--0.015 Å2
L0.9309 °2-0.0357 °2-0.1316 °2-0.0019 °20.0074 °2--1.2365 °2
S-0.0031 Å °-0.0679 Å °0.0069 Å °0.0013 Å °-0.0035 Å °-0.0027 Å °-0.0087 Å °0.021 Å °0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 199
2X-RAY DIFFRACTION1A201

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