SMTL ID : 7or4.1

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B142

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

homo-dimer

Ligands

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 7 residues within 4Å: Chain A: Y.669, S.755, Y.756, Y.787, Y.791, V.836 Ligands: 2YI.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.756 TMO.3: 7 residues within 4Å: Chain B: Y.669, S.755, Y.756, Y.787, Y.791, V.836 Ligands: 2YI.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.669, B:Y.756

2 x 2YI: methyl 3-[4-[(4-bromophenyl)methyl]piperazin-1-yl]carbonyl-5-[(2-ethyl-2-methanoyl-butanoyl)amino]benzoate(Covalent)

2YI.2: 15 residues within 4Å: Chain A: Y.74, F.667, K.685, Y.686, R.688, L.689, W.754, S.755, A.779, N.835, R.868, Y.876, L.880, L.881 Ligands: TMO.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.74, A:F.667, A:R.688, A:L.689, A:W.754, A:A.779, A:N.835, A:Y.876, A:L.880 pi-Cation interactions: A:K.685 2YI.4: 12 residues within 4Å: Chain B: K.685, R.688, W.754, S.755, A.779, D.833, V.836, Y.876, E.877, L.880, L.881 Ligands: TMO.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.688, B:A.779, B:V.836, B:E.877, B:L.880 pi-Cation interactions: B:K.685

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carvalho, L.A.R. et al., Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2021-07-07

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Dipeptidyl peptidase 8

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