SMTL ID : 7oz7.1

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, L84

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x MQ2: ~{N}-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-2-ethyl-2-methanoyl-butanamide(Covalent)

MQ2.1: 14 residues within 4Å: Chain A: F.667, K.685, Y.686, R.688, L.689, W.754, S.755, A.779, D.833, V.836, Y.876, L.880, L.881 Ligands: TMO.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.667, A:R.688, A:L.689, A:A.779, A:V.836, A:Y.876 pi-Stacking: A:W.754, A:W.754 MQ2.3: 13 residues within 4Å: Chain B: F.667, K.685, R.688, L.689, W.754, S.755, A.779, V.836, Y.876, E.877, L.880, L.881 Ligands: TMO.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:A.779, B:V.836, B:E.877, B:L.880 pi-Stacking: B:W.754, B:W.754

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.2: 8 residues within 4Å: Chain A: Y.669, S.755, Y.756, Y.787, Y.791, N.835, V.836 Ligands: MQ2.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.669, A:Y.756 TMO.4: 8 residues within 4Å: Chain B: Y.669, S.755, Y.756, Y.787, Y.791, N.835, V.836 Ligands: MQ2.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.756

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

2021-07-14

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 8

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