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

Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x KBO: 2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide(Covalent)

KBO.1: 16 residues within 4Å: Chain A: R.114, E.229, E.230, H.481, Y.625, Q.629, V.630, K.641, S.711, Y.712, V.737, Y.743, Y.747, N.791, V.792, H.821 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.737, A:Y.747, A:V.792 Hydrogen bonds: A:Y.625, A:Y.712 Water bridges: A:Y.743, A:N.791 pi-Cation interactions: A:R.114 KBO.9: 13 residues within 4Å: Chain B: E.229, E.230, H.481, Y.625, Q.629, V.630, S.711, Y.712, V.737, Y.743, Y.747, V.792, H.821 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.737, B:Y.747, B:V.792 Hydrogen bonds: B:Y.712 pi-Cation interactions: B:R.114

17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: N.293, P.294, K.295, I.296, V.330, E.331 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: K.329, V.330, F.349, L.350, D.351, W.356, Q.358 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: L.504, I.591, F.592, H.593, Y.603 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: M.605, Y.607, L.632, K.638, Y.642, L.645, V.657 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: K.218, E.260, D.262, K.295, A.297, K.299 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: D.406, I.407, F.408, K.484, I.485 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.644, W.710, S.822, I.823, Y.832 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.279 Chain B: H.270, H.793, F.794, F.795 Ligands: EDO.16 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: K.218, E.260, D.262, K.295, A.297 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: P.294, K.295, I.296, V.330, E.331 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: V.330, F.349, L.350, D.351, W.356, L.357, Q.358 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: D.406, I.407, F.408, K.484, I.485 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: M.605, Y.607, L.632, K.638, Y.642, L.645, V.657 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: P.272, R.279, K.280, T.281 Chain B: H.270 Ligands: EDO.10 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: P.810, Y.811 Chain B: W.12, Q.814, H.831, T.835 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: G.560, D.562 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: R.644, W.710, S.822, I.823 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 3 residues within 4Å: Chain A: R.288, F.799 Chain B: E.277 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.277

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

2022-09-28

Peptides

Dipeptidyl peptidase 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Dipeptidyl peptidase 9

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