SMTL ID : 7ayr.1

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B115

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.69 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: S9W.3 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, V.781, Y.787, Y.791, N.835 Ligands: S9W.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.756

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: A.513, I.514, S.516, P.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.516, A:S.516 PO4.5: 5 residues within 4Å: Chain B: A.513, I.514, S.516, P.560, G.561 No protein-ligand interaction detected (PLIP)

2 x S9W: ~{N}-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-4-methanoyl-oxane-4-carboxamide(Covalent)

S9W.3: 12 residues within 4Å: Chain A: K.685, R.688, L.689, W.754, S.755, A.779, D.833, N.835, V.836, Y.876, L.880 Ligands: TMO.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.688, A:L.689, A:A.779, A:Y.876, A:L.880 Hydrogen bonds: A:N.835 pi-Stacking: A:W.754, A:W.754 S9W.6: 15 residues within 4Å: Chain B: F.667, K.685, Y.686, R.688, L.689, W.754, S.755, A.779, D.833, N.835, V.836, Y.876, L.880, L.881 Ligands: TMO.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:A.779, B:Y.876, B:L.880 pi-Stacking: B:W.754, B:W.754

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

2021-06-30

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 8

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