SMTL ID : 9pfl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x 01: (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

01.1: 18 residues within 4Å: Chain A: N.94, S.137, L.138, M.142, V.144, Q.147, Y.150, P.182, G.183, F.184, I.189, L.190, S.192, I.193, M.212, Y.216, T.245 Ligands: NAD.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.150, A:F.184, A:F.184 Hydrogen bonds: A:S.137, A:Y.150 Water bridges: A:T.246, A:T.246 pi-Stacking: A:Y.216, A:Y.216 Halogen bonds: A:I.189 01.12: 18 residues within 4Å: Chain B: N.94, S.137, L.138, M.142, V.144, Q.147, Y.150, P.182, G.183, F.184, I.189, L.190, S.192, I.193, M.212, Y.216, T.245 Ligands: NAD.13 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.138, B:L.138, B:F.184, B:F.184 Hydrogen bonds: B:S.137, B:Y.150 Water bridges: B:T.246, B:T.246 pi-Stacking: B:Y.216, B:Y.216

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

NAD.2: 30 residues within 4Å: Chain A: G.11, A.13, Q.14, G.15, I.16, D.35, W.36, N.37, C.62, D.63, V.64, N.90, A.91, G.92, V.93, I.105, M.135, S.136, S.137, Y.150, K.154, P.182, G.183, F.184, V.185, T.187, A.188, I.189, L.190 Ligands: 01.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.182 Hydrogen bonds: A:G.11, A:A.13, A:Q.14, A:Q.14, A:I.16, A:W.36, A:D.63, A:V.64, A:A.65, A:N.90, A:G.92, A:K.154, A:V.185, A:V.185, A:A.188, A:I.189 Water bridges: A:G.17, A:N.90 pi-Stacking: A:W.36, A:W.36 NAD.13: 30 residues within 4Å: Chain B: G.11, A.13, Q.14, G.15, I.16, D.35, W.36, N.37, C.62, D.63, V.64, N.90, A.91, G.92, V.93, I.105, M.135, S.136, S.137, Y.150, K.154, P.182, G.183, F.184, V.185, T.187, A.188, I.189, L.190 Ligands: 01.12 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:P.182 Hydrogen bonds: B:G.11, B:A.13, B:Q.14, B:Q.14, B:I.16, B:W.36, B:D.63, B:V.64, B:N.90, B:G.92, B:K.154, B:V.185, B:V.185, B:T.187, B:A.188, B:I.189 Water bridges: B:Q.14, B:G.17, B:N.37, B:N.90 pi-Stacking: B:W.36, B:W.36

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 2 residues within 4Å: Chain A: V.93, N.95 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: M.142, K.243 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: K.30, Q.55 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: K.101, Q.104 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain B: V.93, N.95, K.101 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain B: K.243 Ligand excluded by PLIP IOD.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.17: 3 residues within 4Å: Chain B: F.52, E.53, K.56 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain B: Q.43, E.50 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain B: Q.67, Q.68, R.71 Ligand excluded by PLIP IOD.20: 1 residues within 4Å: Chain B: R.71 Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain B: K.101, Q.104 Ligands: IOD.22 Ligand excluded by PLIP IOD.22: 3 residues within 4Å: Chain B: K.101, Q.104 Ligands: IOD.21 Ligand excluded by PLIP IOD.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.7: 4 residues within 4Å: Chain A: N.37, E.39, A.40, Q.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:Q.43 EDO.9: 4 residues within 4Å: Chain A: E.96, K.97, G.200, Q.201 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.201, A:Q.201 Water bridges: A:E.96, B:Y.115 EDO.11: 5 residues within 4Å: Chain A: L.118, S.122, Q.124, M.171, S.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.122 EDO.24: 3 residues within 4Å: Chain B: T.230, I.250, F.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.250 Water bridges: B:T.230, B:D.234 EDO.25: 3 residues within 4Å: Chain B: K.30, H.80, F.81 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.30, B:K.30, B:H.80

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 3 residues within 4Å: Chain A: Q.67, Q.68, R.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.67, A:R.71 Water bridges: A:R.75 GOL.10: 2 residues within 4Å: Chain A: W.36, N.37 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.37 Water bridges: A:L.38, A:L.38, A:L.38

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

2025-09-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

15-hydroxyprostaglandin dehydrogenase [NAD(+)]