SMTL ID : 8cwl.1

Cryo-EM structure of Human 15-PGDH in complex with small molecule SW222746

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NAI.1: 28 residues within 4Å: Chain A: G.11, A.13, Q.14, G.15, I.16, D.35, W.36, 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, I.189, L.190 Ligands: RLD.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.14, A:I.16, A:W.36, A:D.63, A:D.63, A:V.64, A:N.90, A:Y.150, A:K.154, A:V.185, A:V.185, A:T.187, A:I.189 pi-Stacking: A:W.36, A:W.36 NAI.3: 26 residues within 4Å: Chain B: G.11, Q.14, G.15, I.16, D.35, W.36, C.62, D.63, V.64, 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 Ligands: RLD.4 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.182 Hydrogen bonds: B:Q.14, B:W.36, B:D.63, B:D.63, B:V.64, B:Y.150, B:K.154, B:V.185, B:T.187, B:A.188, B:I.189 pi-Stacking: B:W.36, B:W.36

2 x RLD: 2-methyl-6-[7-(piperidine-1-carbonyl)quinoxalin-2-yl]isoquinolin-1(2H)-one(Non-covalent)

RLD.2: 17 residues within 4Å: Chain A: S.137, L.138, A.139, M.142, V.144, Q.147, Y.150, G.183, F.184, I.189, I.193, I.209, M.212, Y.216, T.245, S.247 Ligands: NAI.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.138, A:A.139, A:V.144, A:F.184, A:F.184, A:I.189, A:I.193, A:I.209, A:Y.216 Hydrogen bonds: A:S.137 pi-Stacking: A:F.184, A:Y.216, A:Y.216 RLD.4: 19 residues within 4Å: Chain B: N.94, S.137, L.138, A.139, M.142, V.144, Q.147, Y.150, G.183, F.184, I.189, L.190, I.193, M.212, Y.216, T.245, T.246, S.247 Ligands: NAI.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.138, B:A.139, B:V.144, B:F.184, B:F.184, B:I.189, B:L.190, B:I.193, B:Y.216 Hydrogen bonds: B:S.137, B:T.246 pi-Stacking: B:Y.216, B:Y.216

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

2023-03-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

15-hydroxyprostaglandin dehydrogenase [NAD(+)]