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- PDB-7jr6: H-PDGS complexed with a 2-phenylimidazo[1,2-a]pyridine-6-carboxam... -

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Basic information

Entry
Database: PDB / ID: 7jr6
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 / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Chem-VH4 / Hematopoietic prostaglandin D synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.88 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)48,36610
Polymers46,8562
Non-polymers1,5108
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-64 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.872, 67.997, 69.096
Angle α, β, γ (deg.)90.000, 96.831, 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 , 5 types, 377 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-VH4 / 1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide


Mass: 400.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein diluted to 10mG/mL in 15mM GSH, 50mM TRIS pH 7.5, 50mM NaCl, 25mM MgCl2, 5mM DTT, 1mM EDTA Well Buffer 22% PEG 6K, 1% 1,4 DIOXANE, 10mM DTT, 5% Glycerol, 50mM TRIS pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→37.57 Å / Num. obs: 34104 / % possible obs: 82.54 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.66 Å2 / CC1/2: 0.932 / CC star: 1 / Rmerge(I) obs: 0.06436 / Net I/σ(I): 11.35
Reflection shellResolution: 1.88→1.947 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1625 / CC1/2: 0.592 / CC star: 0.862 / % possible all: 44.44

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.88→37.57 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.4773
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 1764 5.83 %
Rwork0.1763 28499 -
obs0.179 30263 82.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.01 Å2
Refinement stepCycle: LAST / Resolution: 1.88→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 102 369 3715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533463
X-RAY DIFFRACTIONf_angle_d0.67974725
X-RAY DIFFRACTIONf_chiral_restr0.0419515
X-RAY DIFFRACTIONf_plane_restr0.0052600
X-RAY DIFFRACTIONf_dihedral_angle_d19.38581253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.3032770.25941102X-RAY DIFFRACTION42.46
1.93-1.990.2703760.23991454X-RAY DIFFRACTION54.41
1.99-2.050.28361000.22811783X-RAY DIFFRACTION67.08
2.05-2.130.26891160.22462116X-RAY DIFFRACTION79.32
2.13-2.210.27791570.21472352X-RAY DIFFRACTION89.48
2.21-2.310.2641620.20972413X-RAY DIFFRACTION92
2.31-2.430.26821580.19242464X-RAY DIFFRACTION93.04
2.43-2.580.22661500.17222516X-RAY DIFFRACTION95.11
2.59-2.780.241580.17962564X-RAY DIFFRACTION96.56
2.78-3.060.22471650.18122602X-RAY DIFFRACTION97.67
3.06-3.510.22251260.16132159X-RAY DIFFRACTION80.69
3.51-4.420.17931630.13962280X-RAY DIFFRACTION86.08
4.42-37.570.19151560.16132694X-RAY DIFFRACTION98.51
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.769563393860.447769453623-0.5210450991742.863349151141.203734047041.10562173206-0.2217878231990.370285067293-0.423010619353-0.6446350134870.631875155926-0.855085407066-0.3376704073420.4861684375830.0304757972510.180030447681-0.06531072627650.07173948755140.24856568507-0.1624155621910.33453164284662.99402870145.3696684536468.7918991562
23.290747684390.158812858486-0.2751393143673.950521433020.7181698396414.48728238837-0.06004151143980.00220360084404-0.290189032680.02561207910240.1445889968060.447046341783-0.00467758082402-0.211791140608-0.1007476520350.127629415287-0.001553476910720.006180863732230.113361458377-0.02704773871710.18054006492347.7480573482.167697303875.7818525957
33.058810879240.565495710223-0.5367697595473.980371371570.7270549378772.65512220703-0.0405928039311-0.316868361825-0.7267887969690.370262060720.189874956512-0.07113639857480.5664435663960.1265441225890.003376308439850.2374461434310.028855713574-0.05038208416760.171024290494-0.009612970359680.35559760394451.36370104-11.42367908875.528025635
43.43114277487-0.381703567675-0.2432794697872.253850888280.8634621888471.65577338052-0.243511528445-0.414976950821-0.5022047505350.414667742897-0.0510664040510.5287712067610.20834262431-0.275149562870.01997221273960.2268237142650.03066492028060.09412331424170.2300692365960.03207118547670.24197120386341.95700813368.5309667422288.2280038707
50.6293402745090.522061609481-0.04666750148672.85041811149-1.638599455021.769572246120.0061873599181-0.687376346609-0.2441549362110.396327518604-0.0977252665593-0.4412324292240.244892552660.3889969266170.3767015709090.3957652546050.101540129412-0.07127217405270.4490925848260.09873190387690.18838874644563.7943230698.0787135492295.1146656762
62.276988546410.579863085962-0.1083027803122.292240730970.792505540422.208545497380.089940628835-0.8712490970270.6992991205210.5196094333040.03294858469510.126568642458-0.1314989112750.264582909719-0.03514532014410.278871595850.07123455172320.01667789152190.323259641277-0.09273485083870.069201997460452.193942788320.847316884293.0889062534
73.878038300781.359669020630.7046351231479.37700212355-1.371900507728.656765256370.863779328361-0.466707273916-0.6211967974690.747689595284-0.220658735310.471936001360.702900446778-0.530055691787-0.5798614604920.5293989579540.1265170702750.06059348851620.7659117928280.2062677018090.40291092777149.99403720033.7031461672597.9340378736
89.135289893726.342201509858.387758775917.003360932047.865995381929.308196931780.2564902918230.702181544824-0.9477651620620.5511769104760.884518552675-0.105201059719-0.5042933632271.52894957566-0.9688853842180.357060579302-0.002789808100940.06057704381860.6622430998750.1836379599460.76614745429264.3287008579-3.8723539092479.1578434479
94.625699338063.524009827951.788557859138.82787917767-0.8186614228297.43081455676-0.545766261675-0.762971064217-1.184312331090.278254643780.422872326739-1.6250335462-0.4633853225690.3251819123530.04828928673520.367012744060.128597720304-0.1390498789180.370237305083-0.1467743914830.59652111169563.82557424023.1447446972879.6376984144
101.461339829931.401426300571.442832273021.74843227990.9617378144281.886050957330.0815403956785-0.923389706995-0.3009003944960.72509930139-0.469505226561-0.05610150522330.256061028022-0.0429864548486-0.01672564562691.026048126360.2895101274260.6147110791750.5585230627820.578572476588-0.19162680883646.80284935780.12305656612992.7019114753
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 63 )AA0 - 631 - 64
22chain 'A' and (resid 64 through 104 )AA64 - 10465 - 105
33chain 'A' and (resid 105 through 199 )AA105 - 199106 - 200
44chain 'B' and (resid 0 through 104 )BB0 - 1041 - 112
55chain 'B' and (resid 105 through 135 )BB105 - 135113 - 146
66chain 'B' and (resid 136 through 199 )BB136 - 199147 - 210
77chain 'L' and resid 1LE1
88chain 'L' and resid 2LF2
99chain 'G' and resid 1GC1
1010chain 'G' and resid 2GD2

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