SMTL ID : 9goh.1

Crystal structure of DPP4 in complex with sulphostin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: I.158, N.193, T.195, E.196 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.2: 4 residues within 4Å: Chain B: I.158, N.193, T.195, E.196 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.195

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 3 residues within 4Å: Chain A: R.111, I.112, N.114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.111 Water bridges: A:R.111 NAG.4: 5 residues within 4Å: Chain A: E.31, V.42, N.49, S.50, S.51 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: W.151, V.243, N.245 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.649 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: E.37, N.38, N.39, N.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.37, A:N.38, A:N.39, A:N.56 NAG.8: 5 residues within 4Å: Chain A: N.183, T.185, F.186, Q.272, E.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.183, A:T.185, A:E.273 NAG.13: 4 residues within 4Å: Chain B: R.111, I.112, N.114 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.111, B:N.114 NAG.14: 6 residues within 4Å: Chain B: E.31, V.42, N.44, N.49, S.50, S.51 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.42 NAG.15: 3 residues within 4Å: Chain B: W.151, V.243, N.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.245 NAG.16: 3 residues within 4Å: Chain B: E.37, N.39, N.56 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.37 Hydrogen bonds: B:N.39 NAG.17: 1 residues within 4Å: Chain B: N.649 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.655

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

01.9: 8 residues within 4Å: Chain A: R.89, E.169, Y.511, S.594, Y.595, Y.626, N.674, H.704 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.511, A:Y.511, A:Y.595, A:Y.626, A:Y.626, A:Y.626, A:N.674 Water bridges: A:W.593 Salt bridges: A:R.89, A:H.704 01.18: 7 residues within 4Å: Chain B: R.89, E.169, Y.511, S.594, Y.595, Y.626, H.704 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.169, B:Y.511, B:Y.595, B:Y.626, B:H.704 Salt bridges: B:R.89, B:H.704

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: R.25, Y.69, I.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.69, A:I.71 Salt bridges: A:R.25 SO4.11: 3 residues within 4Å: Chain A: R.560, R.561, N.643 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.560, A:R.561 SO4.19: 4 residues within 4Å: Chain B: H.64, Y.82, R.111 Ligands: NAG.13 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.64, B:R.111 SO4.20: 3 residues within 4Å: Chain B: R.560, R.561, N.643 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.561 Salt bridges: B:R.560, B:R.561 SO4.21: 1 residues within 4Å: Chain B: R.435 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.435 Salt bridges: B:R.435

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

EDO.12: 4 residues within 4Å: Chain A: F.59, H.64, S.65, I.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.64, A:I.66

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 4 soluble form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dipeptidyl peptidase 4 soluble form