SMTL ID : 9av8.1

Design and application of synthetic 17B-HSD13 substrates to drug discovery, and to reveal preserved catalytic activity of protective human variants

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: G.44, G.46, H.47, G.48, I.49, G.50, D.68, I.69, V.93, D.94, C.95, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, V.222, T.224, F.226 Ligands: 01.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.49, A:P.219, A:V.222 Hydrogen bonds: A:G.46, A:I.49, A:G.50, A:I.69, A:D.94, A:C.95, A:N.121, A:A.122, A:Y.186, A:V.222, A:T.224, A:T.224, A:T.224 Salt bridges: A:H.47 NAD.3: 25 residues within 4Å: Chain B: G.44, G.46, H.47, G.48, I.49, G.50, D.68, I.69, V.93, D.94, C.95, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, V.222, T.224, F.226 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.49, B:P.219, B:V.222 Hydrogen bonds: B:G.46, B:I.49, B:G.50, B:I.69, B:D.94, B:D.94, B:C.95, B:N.121, B:A.122, B:V.222, B:T.224, B:T.224 Salt bridges: B:H.47

1 x 01: 7-[3-chloro-4-(cyclobutylmethoxy)benzene-1-sulfonamido]-2-methyl-2H-indazole-4-carboxylic acid

01.2: 18 residues within 4Å: Chain A: S.173, V.174, E.178, I.180, L.183, Y.186, V.220, F.221, F.226, T.227, N.229, P.230, S.231, T.232, F.267, L.268, D.271 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.174, A:V.220, A:F.267, A:L.268 Hydrogen bonds: A:S.173, A:F.221, A:S.231, A:S.231, A:T.232, A:T.232 pi-Stacking: A:F.221 Halogen bonds: A:E.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garnsey, M.R. et al., Design and application of synthetic 17B-HSD13 substrates reveals preserved catalytic activity of protective human variants. Nat Commun (2025)

Release Date

2024-11-27

Peptides

Hydroxysteroid 17-beta dehydrogenase 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hydroxysteroid 17-beta dehydrogenase 13