SMTL ID : 7k1e.1

Crystal structure of human insulin degrading enzyme (IDE) in complex with compound BDM_88646

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.79, H.83, E.160 Ligands: VQG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.83, A:E.160, A:E.160 ZN.7: 4 residues within 4Å: Chain B: H.79, H.83, E.160 Ligands: VQG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:H.83, B:E.160, B:E.160

2 x VQG: 3,4-difluoro-N-[(1S)-1-{1-[(2R)-4-(hydroxyamino)-4-oxo-1-(5,6,7,8-tetrahydronaphthalen-2-yl)butan-2-yl]-1H-1,2,3-triazol-4-yl}ethyl]benzamide(Non-covalent)

VQG.2: 19 residues within 4Å: Chain A: H.79, E.82, H.83, F.86, L.87, S.99, S.109, N.110, A.111, E.153, E.160, S.787, E.788, F.791, R.795, T.796, Y.802 Ligands: ZN.1, DIO.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.86, A:F.86, A:L.87 Hydrogen bonds: A:A.111, A:R.795, A:R.795, A:Y.802 pi-Stacking: A:F.86, A:F.791 pi-Cation interactions: A:R.795 VQG.8: 20 residues within 4Å: Chain B: H.79, E.82, H.83, F.86, L.87, S.99, S.103, S.109, N.110, A.111, E.153, E.160, S.787, E.788, F.791, R.795, T.796, Y.802 Ligands: ZN.7, DIO.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.86, B:F.86, B:L.87 Hydrogen bonds: B:E.82, B:R.795, B:R.795, B:Y.802 pi-Stacking: B:F.86, B:F.791 pi-Cation interactions: B:R.795 Halogen bonds: B:S.103

6 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.3: 7 residues within 4Å: Chain A: R.795, Y.802, I.803, V.804, F.805 Ligands: VQG.2, DIO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.804 DIO.4: 5 residues within 4Å: Chain A: H.650, M.654, I.803, F.805 Ligands: DIO.3 No protein-ligand interaction detected (PLIP) DIO.5: 3 residues within 4Å: Chain A: A.169, W.170, F.173 No protein-ligand interaction detected (PLIP) DIO.9: 7 residues within 4Å: Chain B: F.791, R.795, Y.802, I.803, V.804 Ligands: VQG.8, DIO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.804 DIO.10: 5 residues within 4Å: Chain B: H.650, M.654, F.805, I.820 Ligands: DIO.9 No protein-ligand interaction detected (PLIP) DIO.11: 3 residues within 4Å: Chain B: A.169, W.170, F.173 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 12 residues within 4Å: Chain A: Q.771, R.810, A.811, N.812, G.813, R.864, G.880, E.881, S.884, Q.886, R.891, D.892 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.771, A:N.812, A:G.813 Salt bridges: A:E.881 EPE.12: 13 residues within 4Å: Chain B: Q.771, R.810, A.811, N.812, G.813, R.864, G.880, E.881, S.884, Q.886, R.891, D.892, E.895 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.771, B:R.810, B:N.812, B:G.813 Water bridges: B:R.864, B:E.881 Salt bridges: B:E.881

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, W.G. et al., Crystal structure of human insulin degrading enzyme (IDE) in complex with compound 3. To Be Published

Release Date

2021-09-22

Peptides

Insulin-degrading enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Insulin-degrading enzyme

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