SMTL ID : 9gon.2 (1 other biounit)

Crystal structure of DPP9 in complex with sulphostin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x 01: azanyl-oxidanylidene-(sulfoamino)phosphanium

01.1: 9 residues within 4Å: Chain A: R.115, E.230, Y.626, S.712, Y.713, Y.744, N.792, V.793, H.822 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.626, A:Y.713, A:Y.744, A:Y.744, A:Y.744, A:N.792 Water bridges: A:R.115, A:R.115, A:Y.626, A:Y.626, A:Y.626, A:H.822 Salt bridges: A:R.115, A:H.822 01.28: 9 residues within 4Å: Chain B: R.115, E.230, Y.626, S.712, Y.713, Y.744, N.792, V.793, H.822 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.626, B:Y.626, B:Y.713, B:Y.744, B:Y.744, B:Y.744, B:N.792 Water bridges: B:R.115, B:E.230, B:H.822 Salt bridges: B:R.115, B:H.822

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: E.278 Chain B: R.289, A.743, F.796 No protein-ligand interaction detected (PLIP)

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

EDO.3: 6 residues within 4Å: Chain A: N.294, P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.261, D.263, K.296, A.298 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: Y.345, Y.392, L.443 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: K.501, D.502, Y.510, I.520, R.522 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: L.505, I.592, F.593, H.594, Y.604 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: H.507, S.529, H.530, N.635, S.637 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.522, L.523, T.524, T.525, P.526, P.571 Ligand excluded by PLIP EDO.10: 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.11: 4 residues within 4Å: Chain A: G.673, A.674, K.676, Q.678 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: P.354, Q.356, K.676, E.750, R.751 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: K.330, V.331, F.350, D.352, W.357, L.358, Q.359 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: S.704, P.726, Q.727, F.729, K.730, R.781 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: R.289, G.291 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: H.271, V.272, H.794, F.795, F.796 Chain B: R.280 Ligands: EDO.19 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: P.273, R.280, K.281, T.282, F.788 Chain B: H.271 Ligands: EDO.38 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: P.811, Y.812, Q.813 Chain B: W.13, Q.815, H.832, T.836 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: H.271 Chain B: P.273, R.280, K.281, T.282, F.788 Ligands: EDO.16 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: D.407, I.408, F.409, K.485, I.486 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: R.17, S.18, H.21 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: R.645, W.711, S.823, I.824, Y.833 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: K.444, K.462, C.463, P.464 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: R.645, W.711, S.823, I.824, Y.833 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: S.529, S.531, H.544, Y.545, S.546, S.637 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: T.503, R.602, Y.604 Ligands: EDO.34 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: L.505, I.592, F.593, H.594, Y.604 Ligands: EDO.33 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: N.294, P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: E.261, D.263, K.296, A.298 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain B: K.330, F.350, L.351, D.352, W.357, L.358, Q.359 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain A: R.280 Chain B: I.270, H.271, V.272, H.794, F.795, F.796 Ligands: EDO.17 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: R.105, L.109, D.283, S.284, Y.285 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain A: W.13, Q.815, H.832, T.836 Chain B: P.811, Y.812, Q.813 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain A: N.819, C.826, E.828, S.829 Chain B: S.803, I.806, R.807 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: R.24, R.645, G.830, Y.833, E.834 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain B: M.606, Y.608, L.633, Y.643, L.646, V.658 Ligand excluded by PLIP

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

CL.23: 2 residues within 4Å: Chain A: F.412, C.422 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain A: Q.7 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: L.775, K.810 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain B: L.523, T.524, T.525, H.530, Y.557 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain B: E.773, L.775, K.810 Ligand excluded by PLIP

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

NA.27: 3 residues within 4Å: Chain A: E.477, Q.666, G.668 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.477, A:Q.666, A:G.668 Water bridges: A:E.428 NA.29: 6 residues within 4Å: Chain B: W.402, N.404, R.481, Q.630, E.672, Y.752 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.404, B:R.481, B:Y.752 Water bridges: B:R.481 NA.46: 4 residues within 4Å: Chain B: E.428, E.477, Q.666, G.668 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.428, B:Q.666, B:G.668 Water bridges: B:E.428

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

PEG.30: 5 residues within 4Å: Chain A: R.289, M.742, F.796, F.800 Chain B: E.278 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.278

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
C

B
D

Dipeptidyl peptidase 9

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