SMTL ID : 9pfm.1

Crystal structure of human 15-PGDH in complex with small molecule compound 8b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 29 residues within 4Å: Chain A: G.12, A.14, Q.15, G.16, I.17, D.36, W.37, C.63, D.64, V.65, N.91, A.92, G.93, V.94, I.106, M.136, S.137, S.138, Y.151, K.155, P.183, G.184, F.185, V.186, T.188, A.189, I.190, L.191 Ligands: SWL.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.12, A:Q.15, A:Q.15, A:I.17, A:W.37, A:D.64, A:V.65, A:N.91, A:G.93, A:Y.151, A:K.155, A:V.186, A:V.186, A:T.188, A:T.188, A:A.189 Water bridges: A:Q.15, A:G.18, A:N.38, A:N.38, A:N.91 pi-Stacking: A:W.37, A:W.37

1 x 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(Non-covalent)

SWL.2: 19 residues within 4Å: Chain A: N.95, S.138, L.139, M.143, P.144, V.145, Q.148, Y.151, P.183, G.184, F.185, I.190, S.193, I.194, M.213, Y.217, T.246, S.248 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.190, A:I.194 Hydrogen bonds: A:S.138, A:Q.148, A:F.185 pi-Stacking: A:F.185, A:F.185, A:Y.217

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: L.238, A.241, F.253 2 PLIP interactions: 2 interactions with chain A Water bridges: A:I.242, A:Q.254 EDO.4: 4 residues within 4Å: Chain A: K.244, T.246, K.249, H.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.244, A:T.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dodda, L.S. et al., Knowledge and Structure-Based Drug Design of 15-PGDH Inhibitors. J.Med.Chem. (2025)

Release Date

2025-09-03

Peptides

15-hydroxyprostaglandin dehydrogenase [NAD(+)]: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

15-hydroxyprostaglandin dehydrogenase [NAD(+)]