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

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Basic information

Entry
Database: PDB / ID: 9pfm
TitleCrystal structure of human 15-PGDH in complex with small molecule compound 8b
Components15-hydroxyprostaglandin dehydrogenase [NAD(+)]
KeywordsOXIDOREDUCTASE / small molecule inhibitor / 15-PGDH / Prostaglandins E2
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-SWL / 15-hydroxyprostaglandin dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 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(+)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3805
Polymers28,1591
Non-polymers1,2214
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.710, 82.710, 161.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

#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: 28159.230 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SWL / 2-[butyl(oxidanyl)-$l^{3}-sulfanyl]-4-(2,3-dimethylimidazol-4-yl)-6-(1,3-thiazol-2-yl)thieno[2,3-b]pyridin-3-amine


Mass: 433.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N5OS3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 60% v/v Tascimate, pH 7.0

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 1.88→65.503 Å / Num. obs: 27452 / % possible obs: 99.9 % / Redundancy: 21.5 % / Biso Wilson estimate: 31.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.169 / Net I/σ(I): 15.7
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 21.4 % / Rmerge(I) obs: 3.158 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1974 / CC1/2: 0.716 / Rrim(I) all: 3.309 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSv6.2.5data reduction
Aimless0.7.4data scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→65.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.867 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1357 5 %RANDOM
Rwork0.17917 ---
obs0.1816 26026 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.892 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å2-0 Å2
3----3.85 Å2
Refinement stepCycle: 1 / Resolution: 1.88→65.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 80 95 2149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122131
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.82899
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.6647.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8510363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021597
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8623.6991047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8946.6051310
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.844.3021084
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.38742.243271
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 102 -
Rwork0.326 1867 -
obs--99.9 %

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