SMTL ID : 7a3l.1 (1 other biounit)

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, A241

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x QXN: 2-ethyl-2-methanoyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]phenyl]butanamide(Covalent)

QXN.1: 10 residues within 4Å: Chain A: E.275, E.276, Y.669, Q.673, S.755, Y.756, V.781, Y.787, Y.791, H.865 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.781, A:Y.791 Hydrogen bonds: A:Y.669, A:Y.756 QXN.6: 10 residues within 4Å: Chain B: E.275, E.276, Y.669, Q.673, S.755, Y.756, V.781, Y.787, Y.791, H.865 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.781, B:Y.791 Hydrogen bonds: B:Y.756

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.587, H.595, R.680, K.685 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.587, A:K.685 GOL.4: 5 residues within 4Å: Chain A: H.172, P.222, A.223, K.288, A.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.288, A:K.288, A:A.289 GOL.7: 4 residues within 4Å: Chain B: K.587, H.595, R.680, K.685 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.587, B:R.680, B:K.685 GOL.9: 5 residues within 4Å: Chain B: H.172, P.222, A.223, K.288, A.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.288, B:K.288, B:A.289

2 x TMO: trimethylamine oxide(Non-covalent)

TMO.3: 2 residues within 4Å: Chain A: F.667, Y.876 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.876 Water bridges: A:Y.876 TMO.8: 2 residues within 4Å: Chain B: F.667, Y.876 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.876

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

CL.5: 1 residues within 4Å: Chain A: Y.557 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: Y.557 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
A

B
A

Dipeptidyl peptidase 8

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