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- PDB-9pfl: Crystal structure of human 15-PGDH in complex with small molecule... -

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Basic information

Entry
Database: PDB / ID: 9pfl
TitleCrystal structure of human 15-PGDH in complex with small molecule compound 1
Components15-hydroxyprostaglandin dehydrogenase [NAD(+)]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / small molecule inhibitor / 15-PGDH / Prostaglandins E2 / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


15-hydroxyprostaglandin dehydrogenase (NAD+) / 15-hydroxyicosatetraenoate dehydrogenase / regulation of prostaglandin catabolic process / ductus arteriosus closure / ovulation / prostaglandin E receptor activity / parturition / Biosynthesis of Lipoxins (LX) / 15-hydroxyprostaglandin dehydrogenase (NAD+) activity / lipoxygenase pathway ...15-hydroxyprostaglandin dehydrogenase (NAD+) / 15-hydroxyicosatetraenoate dehydrogenase / regulation of prostaglandin catabolic process / ductus arteriosus closure / ovulation / prostaglandin E receptor activity / parturition / Biosynthesis of Lipoxins (LX) / 15-hydroxyprostaglandin dehydrogenase (NAD+) activity / lipoxygenase pathway / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / prostaglandin metabolic process / thrombin-activated receptor signaling pathway / negative regulation of cell cycle / NAD+ binding / positive regulation of vascular associated smooth muscle cell proliferation / transforming growth factor beta receptor signaling pathway / kidney development / female pregnancy / NAD binding / response to estradiol / response to ethanol / response to lipopolysaccharide / basolateral plasma membrane / positive regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / IODIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 15-hydroxyprostaglandin dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShaik, M.M. / Brennan, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Knowledge and Structure-Based Drug Design of 15-PGDH Inhibitors.
Authors: Dodda, L.S. / Campos, S. / Ciccone, D. / Carreiro, S. / Leit, S. / Brennan, D. / Zephyr, J. / Jacques-O'Hagan, S. / Kumar, S. / Kuo, F.S. / Shaik, M.M. / Price, D.J. / Loh, C. / Edmondson, S. ...Authors: Dodda, L.S. / Campos, S. / Ciccone, D. / Carreiro, S. / Leit, S. / Brennan, D. / Zephyr, J. / Jacques-O'Hagan, S. / Kumar, S. / Kuo, F.S. / Shaik, M.M. / Price, D.J. / Loh, C. / Edmondson, S.D. / Tummino, P. / Kaila, N.
History
DepositionJul 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 15-hydroxyprostaglandin dehydrogenase [NAD(+)]
B: 15-hydroxyprostaglandin dehydrogenase [NAD(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,96727
Polymers55,5102
Non-polymers4,45725
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10320 Å2
ΔGint-46 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.695, 107.234, 47.027
Angle α, β, γ (deg.)90, 98.564, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 15-hydroxyprostaglandin dehydrogenase [NAD(+)] / 15-PGDH / Eicosanoid/docosanoid dehydrogenase [NAD(+)] / Prostaglandin dehydrogenase 1 / Short ...15-PGDH / Eicosanoid/docosanoid dehydrogenase [NAD(+)] / Prostaglandin dehydrogenase 1 / Short chain dehydrogenase/reductase family 36C member 1


Mass: 27754.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPGD, PGDH1, SDR36C1 / Production host: Escherichia coli (E. coli)
References: UniProt: P15428, 15-hydroxyprostaglandin dehydrogenase (NAD+), Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 15-hydroxyicosatetraenoate dehydrogenase

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Non-polymers , 6 types, 385 molecules

#2: Chemical ChemComp-A1CH2 / (4S)-7-[7-(4,4-difluoropiperidine-1-carbonyl)-2,3-dihydro-4H-1,4-benzoxazin-4-yl]-2-methyl[1,2,4]triazolo[4,3-a]pyridin-3(2H)-one


Mass: 429.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21F2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaI, 0.1M Bis-Tris Propane, pH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18073 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18073 Å / Relative weight: 1
ReflectionResolution: 1.65→46.546 Å / Num. obs: 53999 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.239 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.079 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2 / Num. unique obs: 2682 / CC1/2: 0.821 / Rrim(I) all: 0.535 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
XDSv6.2.5data reduction
Aimlessv1.12.13data scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.546 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.859 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.117
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2329 2680 5.016 %
Rwork0.1913 50753 -
all0.193 --
obs-53433 97.356 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.289 Å2
Baniso -1Baniso -2Baniso -3
1--0.528 Å20 Å20.117 Å2
2---0.357 Å2-0 Å2
3---0.812 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 196 360 4448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124195
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.7965694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.259526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60810713
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.22310178
X-RAY DIFFRACTIONr_chiral_restr0.1170.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023112
X-RAY DIFFRACTIONr_nbd_refined0.2140.22413
X-RAY DIFFRACTIONr_nbtor_refined0.3210.22899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2392
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1540.223
X-RAY DIFFRACTIONr_mcbond_it1.7822.1272052
X-RAY DIFFRACTIONr_mcangle_it2.4873.8122565
X-RAY DIFFRACTIONr_scbond_it3.2512.4522143
X-RAY DIFFRACTIONr_scangle_it4.8974.3343122
X-RAY DIFFRACTIONr_lrange_it6.18127.5777169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.65-1.6930.2841810.23438210.23640470.9480.96598.88810.23
1.693-1.7390.3151900.27437000.27639350.9240.94798.85640.266
1.739-1.790.261850.19336210.19638320.9570.97799.32150.183
1.79-1.8440.2021900.1734890.17237060.9730.98299.27150.159
1.844-1.9050.3931870.37831020.37935950.860.88591.48820.361
1.905-1.9720.2951480.28930950.2935260.9410.93291.97390.272
1.972-2.0460.3021740.22431200.22833770.9270.96797.54220.205
2.046-2.1290.3261730.2928900.29232430.8910.90694.44960.262
2.129-2.2240.2391580.20928620.21131100.9590.9797.10610.194
2.224-2.3320.3421420.26126690.26529920.9120.93993.95050.235
2.332-2.4580.2121390.15826890.16128450.9720.98499.40250.153
2.458-2.6060.2361240.16825300.17126630.9660.98399.6620.166
2.606-2.7860.2521080.19123600.19425220.9580.97897.85880.191
2.786-3.0080.221060.16922300.17223370.9690.98399.95720.174
3.008-3.2940.1911000.15920550.1621650.980.98699.53810.167
3.294-3.680.1931080.15818250.1619720.9780.98798.02230.168
3.68-4.2450.154970.13316190.13517450.9830.98998.33810.15
4.245-5.1890.167780.12113940.12414730.9820.99299.93210.14
5.189-7.2930.23590.17510610.17811340.9850.98898.76540.188
7.293-46.5460.172330.1996210.1976640.9920.98998.4940.224

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