SMTL ID : 8cvn.1

Cryo-EM Structure of Human 15-PGDH in Complex with Small Molecule SW209415

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.40 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 26 residues within 4Å: Chain A: G.12, A.14, Q.15, I.17, D.36, W.37, C.63, D.64, V.65, N.91, A.92, G.93, V.94, I.106, S.137, S.138, Y.151, K.155, P.183, G.184, F.185, V.186, T.188, I.190, L.191 Ligands: SWL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:P.183 Hydrogen bonds: 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:K.155, A:V.186, A:V.186, A:T.188 pi-Stacking: A:W.37, A:W.37 NAI.3: 26 residues within 4Å: Chain B: G.12, A.14, Q.15, I.17, D.36, W.37, C.63, D.64, V.65, N.91, A.92, G.93, V.94, I.106, S.137, S.138, Y.151, K.155, P.183, G.184, F.185, V.186, T.188, I.190, L.191 Ligands: SWL.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:P.183 Hydrogen bonds: B:Q.15, B:Q.15, B:I.17, B:W.37, B:D.64, B:V.65, B:N.91, B:G.93, B:K.155, B:V.186, B:V.186, B:T.188 pi-Stacking: B:W.37, B:W.37

2 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: 13 residues within 4Å: Chain A: N.95, S.138, L.139, P.144, V.145, Q.148, Y.151, G.184, F.185, I.190, M.213, Y.217 Ligands: NAI.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.95, A:V.145, A:I.190, A:I.190, A:Y.217 Hydrogen bonds: A:S.138, A:Q.148, A:Y.151, A:F.185 pi-Stacking: A:F.185, A:F.185, A:Y.217 SWL.4: 13 residues within 4Å: Chain B: N.95, S.138, L.139, P.144, V.145, Q.148, Y.151, G.184, F.185, I.190, M.213, Y.217 Ligands: NAI.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.95, B:V.145, B:I.190, B:I.190, B:Y.217 Hydrogen bonds: B:S.138, B:Q.148, B:Y.151, B:F.185 pi-Stacking: B:F.185, B:F.185, B:Y.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, W. et al., Small molecule inhibitors of 15-PGDH exploit a physiologic induced-fit closing system. Nat Commun (2023)

Release Date

2023-03-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

15-hydroxyprostaglandin dehydrogenase [NAD(+)]