SMTL ID : 9goc.1 (1 other biounit)

Crystal structure of DPP9 Ser730Ala in complex with sulphostin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x 01: Sulphostin

01.1: 10 residues within 4Å: Chain A: R.115, E.230, E.231, Y.626, Q.630, A.712, Y.744, N.792, H.822 Ligands: EDO.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.115, A:E.230, A:E.231, A:Y.626, A:Y.744, A:N.792, A:H.822, A:H.822 Salt bridges: A:R.115, A:H.822 01.19: 11 residues within 4Å: Chain B: R.115, E.230, E.231, Y.626, Q.630, A.712, Y.744, Y.748, N.792, H.822 Ligands: EDO.20 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.115, B:E.231, B:Y.744, B:N.792, B:H.822, B:H.822 Salt bridges: B:R.115, B:H.822

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

EDO.2: 8 residues within 4Å: Chain A: Y.626, A.712, Y.713, Y.744, Y.748, V.793, H.822 Ligands: 01.1 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: R.645, W.711, S.823, I.824, Y.833 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: M.606, Y.608, L.633, K.639, Y.643, L.646, V.658 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: P.273, R.280, K.281, T.282, F.788 Chain B: H.271 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: W.13, Q.815, H.832, T.836 Chain B: P.811, Y.812 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: F.126, H.127, S.128, P.177 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: K.219, E.261, V.262, D.263, K.296, I.297, A.298 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: N.294, P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: S.265, E.266, V.267, E.268, V.269, R.286 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: K.330, V.331, F.350, L.351, D.352, W.357, L.358, Q.359 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: D.407, I.408, F.409, K.485, I.486 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: Y.448, S.455, E.460 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: L.523, T.524, T.525, H.530, Y.557, P.571 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: V.588, P.589, E.591, K.609 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: R.24, I.824, R.825, C.826, P.827, G.830 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: K.697, Y.698, G.699 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: F.412, Y.514 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain B: Y.626, A.712, Y.713, Y.744, Y.748, V.793, H.822 Ligands: 01.19 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: R.645, W.711, S.823, I.824, Y.833 Ligands: EDO.32 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: M.606, Y.608, L.633, K.639, Y.643, L.646, V.658 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: H.271 Chain B: P.273, R.280, K.281, F.788 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: S.265, E.266, V.267, E.268, V.269, R.286 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: N.294, P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: E.261, V.262, D.263, K.296, A.298 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: V.331, F.350, L.351, D.352, W.357, Q.359 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: D.407, I.408, F.409, K.485, I.486 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: R.24, R.645, I.824, G.830, Y.833, E.834 Ligands: EDO.21 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: V.214, L.215, D.217, P.218, R.286 Ligand excluded by PLIP

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

PEG.27: 4 residues within 4Å: Chain A: R.289, F.796 Chain B: E.278, R.280 No protein-ligand interaction detected (PLIP) PEG.29: 7 residues within 4Å: Chain B: F.6, H.611, A.612, H.619, S.651, L.652, G.653 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.614 Water bridges: B:A.612

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.28: 7 residues within 4Å: Chain A: E.278, R.280 Chain B: R.289, V.740, M.742, F.796, F.800 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sewald, L. et al., Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors. Nat Commun (2025)

Release Date

2025-07-16

Peptides

Dipeptidyl peptidase 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 9

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