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

DPP8 IN COMPLEX WITH LIGAND ICeD-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

14 x D06: (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one(Non-covalent)(Non-functional Binders)

D06.1: 17 residues within 4Å: Chain A: R.160, E.275, E.276, H.525, Y.669, Q.673, V.674, S.755, Y.756, A.779, V.781, W.784, Y.787, Y.791, N.835, V.836, H.865 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.674, A:Y.756, A:V.781, A:W.784, A:Y.791, A:V.836 Hydrogen bonds: A:R.160, A:E.275, A:E.275, A:Y.787, A:N.835 Water bridges: A:S.755 D06.2: 10 residues within 4Å: Chain A: F.667, K.685, R.688, L.689, W.754, H.865, S.866, I.867, Y.876, L.880 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.688, A:L.689, A:W.754, A:W.754, A:L.880 Water bridges: A:I.867 pi-Stacking: A:W.754, A:H.865 D06.3: 7 residues within 4Å: Chain A: A.141, T.142, L.143, S.184, Y.187, P.204 Ligands: D06.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.141, A:L.143 Hydrogen bonds: A:Y.187 D06.4: 1 residues within 4Å: Ligands: D06.3 No protein-ligand interaction detected (PLIP) D06.5: 3 residues within 4Å: Chain A: E.803, Q.804 Ligands: D06.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.803 D06.6: 8 residues within 4Å: Chain A: D.747, R.748, R.773, N.887, L.888, A.893, A.894, V.897 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.748, A:R.773, A:A.894, A:V.897 D06.7: 6 residues within 4Å: Chain A: E.803, Q.804, Y.807, M.813, F.847 Ligands: D06.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.803, A:Q.804, A:Y.807, A:F.847 D06.13: 17 residues within 4Å: Chain B: R.160, E.275, E.276, H.525, Y.669, Q.673, V.674, S.755, Y.756, A.779, V.781, W.784, Y.787, Y.791, N.835, V.836, H.865 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.674, B:Y.756, B:V.781, B:W.784, B:Y.791, B:V.836 Hydrogen bonds: B:R.160, B:E.275, B:Y.787, B:N.835 Water bridges: B:S.755 D06.14: 10 residues within 4Å: Chain B: F.667, K.685, R.688, L.689, W.754, H.865, S.866, I.867, Y.876, L.880 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:R.688, B:L.689, B:W.754, B:W.754, B:L.880 Water bridges: B:I.867 pi-Stacking: B:W.754, B:H.865 D06.15: 7 residues within 4Å: Chain B: A.141, T.142, L.143, S.184, Y.187, P.204 Ligands: D06.16 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.141, B:L.143 Hydrogen bonds: B:Y.187 D06.16: 1 residues within 4Å: Ligands: D06.15 No protein-ligand interaction detected (PLIP) D06.17: 3 residues within 4Å: Chain B: E.803, Q.804 Ligands: D06.19 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.803 D06.18: 8 residues within 4Å: Chain B: D.747, R.748, R.773, N.887, L.888, A.893, A.894, V.897 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.748, B:R.773, B:A.894, B:V.897 D06.19: 6 residues within 4Å: Chain B: E.803, Q.804, Y.807, M.813, F.847 Ligands: D06.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.803, B:Q.804, B:Y.807, B:F.847

10 x TMO: trimethylamine oxide(Non-covalent)

TMO.8: 3 residues within 4Å: Chain A: A.513, S.516, P.560 No protein-ligand interaction detected (PLIP) TMO.9: 3 residues within 4Å: Chain A: F.83, M.84, Y.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.169 TMO.10: 1 residues within 4Å: Chain A: W.132 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.132, A:W.132 TMO.11: 3 residues within 4Å: Chain A: Y.56, L.64, S.694 No protein-ligand interaction detected (PLIP) TMO.12: 2 residues within 4Å: Chain A: D.800, E.803 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.800 Salt bridges: A:D.800, A:E.803 TMO.20: 3 residues within 4Å: Chain B: A.513, S.516, P.560 No protein-ligand interaction detected (PLIP) TMO.21: 3 residues within 4Å: Chain B: F.83, M.84, Y.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.169 TMO.22: 1 residues within 4Å: Chain B: W.132 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.132, B:W.132 TMO.23: 3 residues within 4Å: Chain B: Y.56, L.64, S.694 No protein-ligand interaction detected (PLIP) TMO.24: 2 residues within 4Å: Chain B: D.800, E.803 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.800 Salt bridges: B:D.800, B:E.803

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moore, K.P. et al., A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells. Acs Chem.Biol. (2022)

Release Date

2022-10-05

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dipeptidyl peptidase 8

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