SMTL ID : 9gon.1 (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 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.626, A:Y.626, A:Y.713, A:Y.744, A:Y.744, A:Y.744, A:N.792 Water bridges: A:R.115, A:E.230, A:H.822 Salt bridges: A:R.115, A:H.822 01.24: 9 residues within 4Å: Chain B: R.115, E.230, Y.626, S.712, Y.713, Y.744, N.792, V.793, H.822 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.626, B:Y.713, B:Y.744, B:Y.744, B:Y.744, B:N.792 Water bridges: B:Y.626, B:Y.626, B:H.822 Salt bridges: B:R.115, B:H.822

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

PEG.2: 5 residues within 4Å: Chain A: E.278, R.280 Chain B: R.289, M.742, F.796 No protein-ligand interaction detected (PLIP) PEG.26: 3 residues within 4Å: Chain B: K.10, H.11, S.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.12 PEG.32: 6 residues within 4Å: Chain A: R.289, M.742, F.796, F.800 Chain B: E.278, R.280 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.278

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

EDO.3: 4 residues within 4Å: Chain A: H.50, E.72, L.85, S.86 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: F.126, H.127, S.128 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.261, V.262, D.263, K.296, A.298 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: S.265, E.266, V.267, E.268, V.269, R.286 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: H.271 Chain B: R.280, K.281, T.282 Ligand excluded by PLIP EDO.8: 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.9: 5 residues within 4Å: Chain A: R.105, L.109, D.283, S.284, Y.285 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: N.294, P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: D.407, I.408, F.409, K.485, I.486 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: P.413, S.415, E.418 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: I.592, H.594, Y.604 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: P.275, L.277, E.278, N.819 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.811, Y.812 Chain B: W.13, Q.815, H.832, T.836 Ligand excluded by PLIP EDO.16: 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.17: 5 residues within 4Å: Chain A: K.501, D.502, Y.510, I.520, R.522 Ligand excluded by PLIP EDO.18: 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.19: 5 residues within 4Å: Chain A: R.645, W.711, S.823, I.824, Y.833 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: F.6, H.611, H.619, S.651, L.652, G.653 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: R.645, W.711, S.823, I.824, Y.833 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: K.33, A.34, H.36, H.544 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: H.507, S.529, S.637 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain B: E.261, V.262, D.263, K.296, I.297, A.298 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: P.295, K.296, I.297, V.331, E.332 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: F.593, H.594, K.697 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: P.354, Q.356, K.676, E.750, R.751, D.754 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: L.703, S.704, Q.727 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: L.109, D.283, S.284, Y.285 Ligand excluded by PLIP EDO.39: 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.40: 6 residues within 4Å: Chain A: N.819, E.828, S.829 Chain B: S.803, I.806, R.807 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: R.24, R.645, G.830, Y.833, E.834 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain A: N.780, Y.844 Chain B: H.839, E.843, Y.844 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: D.407, I.408, F.409, K.485, I.486 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain B: V.588, H.611, A.612 Ligand excluded by PLIP EDO.45: 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.46: 4 residues within 4Å: Chain B: R.662, R.670, F.671, A.674 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: Y.395, E.396, K.462, I.465, E.468 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain B: K.330, F.350, L.351, D.352, W.357, Q.359 Ligand excluded by PLIP

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

CL.20: 2 residues within 4Å: Chain A: L.775, K.810 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: R.24, I.824, R.825, C.826, P.827 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain A: R.522, T.524 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: K.618, I.701, L.703 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: K.725, P.726, Q.727, V.728 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain B: L.109, R.113, F.226 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain B: E.773, L.775, K.810 Ligand excluded by PLIP

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

NA.22: 4 residues within 4Å: Chain A: E.428, 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.672 NA.51: 3 residues within 4Å: Chain B: E.477, Q.666, G.668 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.477, B:Q.666, B:G.668

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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