SMTL ID : 7a3k.1 (1 other biounit)

Crystal structure of DPP8 in complex with a b-lactam based inhibitor, A296.1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 6 residues within 4Å: Chain A: Y.669, S.755, Y.756, Y.787, Y.791, V.836 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.669, A:Y.756 Water bridges: A:Y.669 TMO.8: 7 residues within 4Å: Chain B: Y.669, S.755, Y.756, Y.787, Y.791, N.835, V.836 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.669, B:Y.756 Water bridges: B:Y.791

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: Y.557 Ligand excluded by PLIP CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: W.132 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: S.516 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain B: Y.557 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: S.516 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: Q.274, E.275, D.278, Y.280 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.275 NA.11: 4 residues within 4Å: Chain B: Q.274, E.275, D.278, Y.280 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.274, B:Y.280

2 x QX8: 1-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]azetidin-2-one(Non-covalent)

QX8.7: 12 residues within 4Å: Chain A: F.667, K.685, Y.686, R.688, L.689, W.754, H.865, S.866, I.867, Y.876, L.880, L.881 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.688, A:L.689, A:W.754, A:W.754, A:W.754, A:Y.876, A:L.880 pi-Stacking: A:W.754 QX8.12: 13 residues within 4Å: Chain B: F.667, K.685, Y.686, R.688, L.689, W.754, D.833, H.865, S.866, I.867, Y.876, L.880, L.881 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:W.754, B:W.754, B:W.754, B:Y.876 Hydrogen bonds: B:H.865 pi-Stacking: B:W.754

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fehr, L. et al., Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9. To Be Published

Release Date

2021-07-07

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Dipeptidyl peptidase 8

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