SMTL ID : 7a3i.1 (1 other biounit)

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, LMC375

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 9 residues within 4Å: Chain A: Y.669, S.755, Y.756, V.781, Y.787, Y.791, N.835, V.836 Ligands: QXH.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.787, A:Y.787 TMO.5: 9 residues within 4Å: Chain B: Y.669, S.755, Y.756, V.781, Y.787, Y.791, N.835, V.836 Ligands: QXH.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.787

2 x QXH: ~{N}-[3,5-bis[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-2-ethyl-2-methanoyl-butanamide(Covalent)

QXH.2: 22 residues within 4Å: Chain A: F.667, K.685, Y.686, R.688, L.689, W.754, S.755, A.779, D.833, N.835, V.836, Y.860, P.861, Q.862, S.872, G.873, Y.876, E.877, L.880, L.881 Chain B: R.850 Ligands: TMO.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:R.688, A:L.689, A:A.779, A:N.835, A:V.836, A:Y.860, A:E.877, A:L.880 pi-Stacking: A:W.754, A:W.754 pi-Cation interactions: A:Y.74 QXH.6: 22 residues within 4Å: Chain A: R.850 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.860, P.861, Q.862, S.872, G.873, Y.876, E.877, L.880, L.881 Ligands: TMO.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:A.779, B:N.835, B:V.836, B:Y.860, B:E.877, B:L.880 pi-Stacking: B:W.754, B:W.754 pi-Cation interactions: B:Y.74

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

NA.3: 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:Y.280 NA.7: 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:Y.280, B:Y.280

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

CL.4: 1 residues within 4Å: Chain A: S.516 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: S.516 Ligand excluded by PLIP

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

2021-06-30

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dipeptidyl peptidase 8

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