SMTL ID : 4nxo.2 (1 other biounit)

Crystal Structure of Insulin Degrading Enzyme in complex with BDM44768

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.79, H.83, E.160 Ligands: 2H7.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:H.83, A:E.160, A:E.160

1 x 2H7: 4-fluoro-N-({1-[(2R)-4-(hydroxyamino)-1-(naphthalen-2-yl)-4-oxobutan-2-yl]-1H-1,2,3-triazol-4-yl}methyl)benzamide(Non-covalent)

2H7.2: 17 residues within 4Å: Chain A: H.79, Q.82, H.83, F.86, S.99, S.109, N.110, A.111, E.160, S.787, E.788, F.791, R.795, Y.802, I.803, V.804 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.788, A:F.791, A:Y.802 Hydrogen bonds: A:Q.82, A:A.111, A:R.795 pi-Stacking: A:H.83, A:F.791 Halogen bonds: A:S.787, A:S.787

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 12 residues within 4Å: Chain A: Q.294, Y.297, N.300, H.303, Q.334, N.389, Y.415, A.423, E.424, Y.425, L.426, L.427 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.300, A:Q.334, A:N.389, A:Y.415 Water bridges: A:E.424

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: V.331, G.332, G.333, Q.334, K.335, I.345 No protein-ligand interaction detected (PLIP) PEG.5: 10 residues within 4Å: Chain A: L.172, L.175, E.176, T.179, Y.273, I.275, Y.285, T.287, R.448, A.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.176, A:E.176, A:R.448 PEG.6: 7 residues within 4Å: Chain A: Y.555, S.561, N.593, T.594, I.595, Y.637, L.671 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.593, A:N.593, A:Y.637 Water bridges: A:I.595 PEG.9: 3 residues within 4Å: Chain A: A.169, W.170, F.173 No protein-ligand interaction detected (PLIP)

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

EDO.7: 6 residues within 4Å: Chain A: H.650, M.654, I.803, F.805, R.818, I.820 No protein-ligand interaction detected (PLIP) EDO.8: 5 residues within 4Å: Chain A: E.399, R.400, G.403, Y.404, K.870 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.400, A:R.400, A:K.870, A:K.870

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

EPE.10: 10 residues within 4Å: Chain A: Q.771, R.810, A.811, N.812, G.813, G.880, E.881, S.884, Q.886, R.891 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.771, A:N.812, A:G.813 Water bridges: A:E.780, A:R.810 Salt bridges: A:E.881

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

DIO.11: 7 residues within 4Å: Chain A: N.283, Y.285, T.329, V.331, N.347, V.348, D.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deprez-Poulain, R. et al., Catalytic site inhibition of insulin-degrading enzyme by a small molecule induces glucose intolerance in mice. Nat Commun (2015)

Release Date

2015-10-07

Peptides

Insulin-degrading enzyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Insulin-degrading enzyme

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