SMTL ID : 7a3g.1

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, 91

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

4 x TMO: trimethylamine oxide(Non-covalent)

TMO.1: 9 residues within 4Å: Chain A: T.317, R.324, R.325, A.326 Chain B: H.315, T.317, A.326, H.837 Ligands: TMO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.317, B:T.317, B:T.317 TMO.3: 3 residues within 4Å: Chain A: W.754, I.867 Ligands: QXT.10 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.754, A:W.754 TMO.12: 8 residues within 4Å: Chain A: H.315, T.317, H.837 Chain B: T.317, R.324, R.325, A.326 Ligands: TMO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.837 TMO.14: 5 residues within 4Å: Chain B: W.754, S.866, I.867, Y.876 Ligands: QXT.21 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.754, B:W.754

2 x QXQ: ~{N}-[3-(7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-6-ylmethyl)phenyl]-2-ethyl-2-methanoyl-butanamide(Covalent)

QXQ.2: 17 residues within 4Å: Chain A: E.275, E.276, F.277, D.278, R.380, I.449, R.524, H.525, Y.669, Q.673, S.755, Y.756, V.781, Y.787, N.835, H.865 Ligands: QXT.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.781, A:N.835 Hydrogen bonds: A:Y.669, A:Y.756 Salt bridges: A:D.278 QXQ.13: 17 residues within 4Å: Chain B: E.275, E.276, F.277, D.278, R.380, I.449, R.524, H.525, Y.669, Q.673, S.755, Y.756, V.781, Y.787, N.835, H.865 Ligands: QXT.21 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.781, B:N.835 Hydrogen bonds: B:Y.756 Salt bridges: B:D.278

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: H.595, R.680, F.681 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.680, A:F.681, A:K.682 GOL.5: 3 residues within 4Å: Chain A: P.222, A.223, A.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.222, A:A.289 GOL.15: 3 residues within 4Å: Chain B: H.595, R.680, F.681 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.680, B:R.680, B:F.681 Water bridges: B:K.685 GOL.16: 5 residues within 4Å: Chain B: H.172, P.222, A.223, P.287, K.288 No protein-ligand interaction detected (PLIP)

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 2 residues within 4Å: Chain A: D.82, Y.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.169 PO4.7: 2 residues within 4Å: Chain A: Y.389, L.486 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.389 PO4.8: 6 residues within 4Å: Chain A: A.513, I.514, T.515, S.516, P.560, G.561 No protein-ligand interaction detected (PLIP) PO4.9: 7 residues within 4Å: Chain A: S.265, V.268, A.269, T.270, F.271, Q.274, E.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.234, A:S.265, A:F.271, A:Q.274 PO4.17: 2 residues within 4Å: Chain B: M.84, Y.169 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.169, B:Y.169 PO4.18: 2 residues within 4Å: Chain B: Y.389, L.486 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.389 PO4.19: 5 residues within 4Å: Chain B: A.513, I.514, S.516, P.560, G.561 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.560 PO4.20: 5 residues within 4Å: Chain B: N.234, V.268, A.269, T.270, E.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.269, B:F.271

2 x QXT: 1-[3-(7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-6-ylmethyl)phenyl]-3,3-diethyl-azetidine-2,4-dione(Non-covalent)

QXT.10: 13 residues within 4Å: Chain A: F.667, Y.669, K.685, Y.686, R.688, L.689, L.692, W.754, Y.876, E.877, L.880 Ligands: QXQ.2, TMO.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.667, A:R.688, A:L.689, A:W.754, A:Y.876, A:E.877, A:L.880 Hydrogen bonds: A:K.685 pi-Stacking: A:F.667 QXT.21: 13 residues within 4Å: Chain B: F.667, Y.669, K.685, Y.686, R.688, L.689, L.692, W.754, Y.876, E.877, L.880 Ligands: QXQ.13, TMO.14 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.667, B:R.688, B:L.689, B:W.754, B:Y.876, B:E.877, B:L.880 Hydrogen bonds: B:K.685 pi-Stacking: B:F.667

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

CL.11: 1 residues within 4Å: Chain A: Y.557 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: F.456, Y.557 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carvalho, L.A.R. et al., Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2021-06-30

Peptides

Dipeptidyl peptidase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Dipeptidyl peptidase 8

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