SMTL ID : 7svo.2 (1 other biounit)

DPP8 IN COMPLEX WITH LIGAND ICeD-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

2 x CW8: (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile(Covalent)

CW8.1: 13 residues within 4Å: Chain A: R.165, E.280, E.281, Y.674, Q.678, S.760, Y.761, V.786, Y.792, Y.796, N.840, V.841, H.870 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.678, A:V.786, A:Y.792, A:V.841 Hydrogen bonds: A:R.165, A:E.280, A:E.280, A:Y.674, A:Y.761, A:Y.792, A:N.840 CW8.8: 13 residues within 4Å: Chain B: R.165, E.280, E.281, Y.674, Q.678, S.760, Y.761, V.786, Y.792, Y.796, N.840, V.841, H.870 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Q.678, B:V.786, B:Y.792, B:V.841 Hydrogen bonds: B:R.165, B:E.280, B:Y.761, B:Y.792, B:N.840

12 x TMO: trimethylamine oxide(Non-covalent)

TMO.2: 2 residues within 4Å: Chain A: D.805, E.808 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.808 Salt bridges: A:E.808 TMO.3: 1 residues within 4Å: Chain A: Y.174 No protein-ligand interaction detected (PLIP) TMO.4: 2 residues within 4Å: Chain A: R.155, E.156 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.156 TMO.5: 1 residues within 4Å: Chain A: L.491 No protein-ligand interaction detected (PLIP) TMO.6: 3 residues within 4Å: Chain A: Y.61, L.69, S.699 No protein-ligand interaction detected (PLIP) TMO.7: 2 residues within 4Å: Chain A: Y.674, Y.691 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.674 TMO.9: 2 residues within 4Å: Chain B: D.805, E.808 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.808 Salt bridges: B:E.808 TMO.10: 1 residues within 4Å: Chain B: Y.174 No protein-ligand interaction detected (PLIP) TMO.11: 2 residues within 4Å: Chain B: R.155, E.156 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.156 TMO.12: 1 residues within 4Å: Chain B: L.491 No protein-ligand interaction detected (PLIP) TMO.13: 3 residues within 4Å: Chain B: Y.61, L.69, S.699 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.61 TMO.14: 2 residues within 4Å: Chain B: Y.674, Y.691 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:Y.674

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
B

B
B

Dipeptidyl peptidase 8

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