SMTL ID : 7a3j.1 (1 other biounit)

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A272

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

QXK.1: 19 residues within 4Å: Chain A: F.667, K.685, R.688, L.689, L.692, H.752, W.754, S.755, A.779, D.833, V.836, H.865, S.866, I.867, Y.876, E.877, L.880, L.881 Ligands: TMO.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.667, A:F.667, A:R.688, A:L.689, A:L.689, A:L.692, A:A.779, A:V.836, A:I.867, A:E.877, A:L.880, A:L.881 Hydrogen bonds: A:H.865 pi-Stacking: A:W.754, A:W.754 pi-Cation interactions: A:H.752 QXK.4: 15 residues within 4Å: Chain B: F.667, K.685, R.688, L.689, L.692, H.752, W.754, S.755, D.833, V.836, Y.876, E.877, L.880, L.881 Ligands: TMO.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.667, B:R.688, B:R.688, B:L.689, B:W.754, B:V.836, B:E.877, B:L.880, B:L.881 pi-Stacking: B:W.754 pi-Cation interactions: B:H.752

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.2: 7 residues within 4Å: Chain A: Y.669, S.755, Y.756, Y.787, Y.791, V.836 Ligands: QXK.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.669 TMO.5: 8 residues within 4Å: Chain B: Y.669, S.755, Y.756, Y.787, Y.791, N.835, V.836 Ligands: QXK.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.669, B:Y.669

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

CL.3: 1 residues within 4Å: Chain A: Y.169 Ligand excluded by PLIP CL.6: 1 residues within 4Å: Chain B: Y.169 Ligand excluded by PLIP

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
C

B
B

Dipeptidyl peptidase 8

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