9PFL | pdb_00009pfl

Crystal structure of human 15-PGDH in complex with small molecule compound 1

PDB DOI: https://doi.org/10.2210/pdb9PFL/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-05 Released: 2025-09-10
Deposition Author(s): Shaik, M.M., Brennan, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Knowledge and Structure-Based Drug Design of 15-PGDH Inhibitors.

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.

(2025) J Med Chem 68: 18436-18462

PubMed: 40864846 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c01231
Primary Citation Related Structures:
9PFL, 9PFM

PubMed Abstract:
PGE2 plays important roles in immune cell function and in potentiating tissue regeneration. 15-PGDH is the key enzyme involved in inactivation of PGE2 and its inhibition therefore provides valuable therapeutic opportunity. We have solved the first cocrystal structure of 15-PGDH bound to small molecule inhibitors, enabling us to efficiently investigate and understand the key functionalities required for potency. Rational structure-based design coupled with a host of advanced computational methods, including FEP+ and WaterMap, were used to develop novel series of 15-PGDH inhibitors. Of note, a machine-learning (ML) model trained with potencies predicted by FEP+ yielded a powerful tool to guide synthetic priority across a large virtual chemical library. Ultimately, a lead compound demonstrated elevation of colonic PGE2 following IP administration in mice, consistent with our therapeutic hypothesis.

Organizational Affiliation

Nimbus Therapeutics, Boston, Massachusetts 02210, United States.

Macromolecule Content

Total Structure Weight: 59.97 kDa
Atom Count: 4,494
Modeled Residue Count: 510
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
15-hydroxyprostaglandin dehydrogenase [NAD(+)]	A, B	255	Homo sapiens	Mutation(s): 0 Gene Names: HPGD, PGDH1, SDR36C1 EC: 1.1.1.141 (PDB Primary Data), 1.1.1 (PDB Primary Data), 1.1.1.232 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P15428 (Homo sapiens) Explore P15428 Go to UniProtKB: P15428
PHAROS: P15428 GTEx: ENSG00000164120
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15428
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain D [auth A]	D [auth A], O [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain O [auth B]
A1CH2 (Subject of Investigation/LOI) Query on A1CH2 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain C [auth A]	C [auth A], N [auth B]	(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 C₂₁ H₂₁ F₂ N₅ O₃ BSUIDNIGESUTFD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] P [auth B] E [auth A], F [auth A], G [auth A], H [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A]	J [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth B]	AA [auth B], I [auth A], K [auth A], M [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Z [auth B]