SMTL ID : 7ayq.1

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, B114

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 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: S9Z.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.669, A:Y.756 TMO.5: 8 residues within 4Å: Chain B: Y.669, S.755, Y.756, V.781, Y.787, Y.791, N.835 Ligands: S9Z.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.756

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

PO4.2: 5 residues within 4Å: Chain A: A.513, I.514, T.515, S.516, P.560 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.516, A:S.516, A:S.516 PO4.6: 5 residues within 4Å: Chain B: A.513, I.514, T.515, S.516, P.560 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.513

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: H.595, R.680, K.682, K.685 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.680, A:K.682 GOL.7: 5 residues within 4Å: Chain B: H.595, R.680, F.681, K.682, K.685 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.680, B:F.681, B:K.682

2 x S9Z: ~{N}-[3-[4-[(4-bromophenyl)methyl]piperazin-1-yl]carbonylphenyl]-2-ethyl-2-methanoyl-butanamide(Covalent)

S9Z.4: 16 residues within 4Å: Chain A: Y.74, F.667, K.685, Y.686, R.688, L.689, W.754, S.755, A.779, D.833, V.836, Y.876, E.877, L.880, L.881 Ligands: TMO.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.74, A:R.688, A:L.689, A:A.779, A:V.836, A:E.877, A:L.880 pi-Stacking: A:W.754, A:W.754 Halogen bonds: A:E.877 S9Z.8: 13 residues within 4Å: Chain B: K.685, Y.686, R.688, L.689, W.754, S.755, A.779, D.833, V.836, Y.876, E.877, L.880 Ligands: TMO.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:A.779, B:V.836, B:L.880 pi-Stacking: B:W.754, B:W.754 pi-Cation interactions: B:Y.74 Halogen bonds: B:E.877

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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