SMTL ID : 9av4.1

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 2.09 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.44, G.46, H.47, G.48, I.49, D.68, I.69, V.93, D.94, C.95, G.96, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: 01.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.219 Hydrogen bonds: A:G.44, A:G.44, A:G.46, A:I.49, A:I.69, A:D.94, A:C.95, A:G.96, A:N.121, A:Y.186, A:K.190, A:V.222, A:V.222, A:T.224, A:T.224 Water bridges: A:H.47, A:G.50, A:N.70, A:N.121, A:G.225 Salt bridges: A:H.47 NAD.3: 27 residues within 4Å: Chain B: G.44, G.46, H.47, G.48, I.49, D.68, I.69, V.93, D.94, C.95, G.96, N.121, A.122, G.123, I.144, V.171, A.172, S.173, Y.186, K.190, P.219, V.220, F.221, V.222, T.224, F.226 Ligands: 01.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.219 Hydrogen bonds: B:G.44, B:G.46, B:I.49, B:I.69, B:D.94, B:C.95, B:G.96, B:N.121, B:K.190, B:V.222, B:V.222, B:T.224 Water bridges: B:G.50, B:N.121 Salt bridges: B:H.47

2 x 01: 4-(3,4-dichlorobenzene-1-sulfonamido)-2-fluorobenzoic acid

01.2: 21 residues within 4Å: Chain A: S.173, V.174, C.175, E.178, G.179, I.180, L.183, Y.186, P.219, V.220, F.221, F.226, T.227, N.229, P.230, S.231, T.232, L.234, Y.264, L.268 Ligands: NAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.180, A:Y.264 Hydrogen bonds: A:S.173, A:S.173, A:F.221, A:S.231, A:S.231, A:T.232 Halogen bonds: A:E.178, A:G.179, A:P.219 01.4: 19 residues within 4Å: Chain B: S.173, V.174, C.175, E.178, I.180, L.183, Y.186, P.219, V.220, F.221, F.226, T.227, N.229, P.230, S.231, T.232, Y.264, L.268 Ligands: NAD.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.174, B:I.180, B:Y.264 Hydrogen bonds: B:S.173, B:S.173, B:Y.186, B:F.221, B:T.227, B:S.231, B:S.231, B:T.232 Halogen bonds: B:E.178, B:P.219

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

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