SMTL ID : 8abx.1

Crystal structure of IDO1 in complex with Apoxidole-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 5 residues within 4Å: Chain A: W.257, D.259, P.260, K.261 Ligands: PGE.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.261 PG4.5: 5 residues within 4Å: Chain A: R.109, G.255, F.256, W.257, E.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.255

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 3 residues within 4Å: Chain A: D.259, K.261 Ligands: PG4.1 No protein-ligand interaction detected (PLIP) PGE.3: 10 residues within 4Å: Chain A: Q.33, N.35, L.36, P.37, D.38, H.73, L.74, T.75, D.76, S.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.36, A:T.75, A:S.79 Water bridges: A:D.38 PGE.4: 8 residues within 4Å: Chain A: I.71, D.72, L.74, T.75, D.76, H.77, Q.80, K.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.72, A:Q.80, A:Q.80, A:K.121 PGE.6: 6 residues within 4Å: Chain A: K.105, V.106, V.252, E.258, D.259, P.260 No protein-ligand interaction detected (PLIP) PGE.7: 7 residues within 4Å: Chain A: D.42, F.45, I.46, E.61, R.62, K.65, L.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.62

1 x N39: O1-tert-butyl O2-ethyl O5-methyl (E,5R)-5-(1-methylindol-2-yl)-5-[(4-methylphenyl)sulfonylamino]pent-2-ene-1,2,5-tricarboxylate(Non-covalent)

N39.8: 30 residues within 4Å: Chain A: Y.130, C.133, V.134, F.167, F.168, S.171, V.174, E.175, F.218, I.221, F.230, R.235, L.238, G.266, S.267, A.268, G.269, Q.270, S.271, F.274, Q.275, L.296, R.347, H.350, I.353, V.354, Y.357, I.358, L.388 Ligands: N2U.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.130, A:V.134, A:F.167, A:F.167, A:I.221, A:F.274, A:F.274, A:Q.275, A:I.353, A:Y.357 Salt bridges: A:H.350

1 x N2U: O2-tert-butyl O3-ethyl O6-methyl (2S,6R)-6-(1-methylindol-2-yl)-2,5-dihydro-1H-pyridine-2,3,6-tricarboxylate(Non-covalent)

N2U.9: 27 residues within 4Å: Chain A: Y.130, C.133, V.134, F.167, F.168, S.171, V.174, E.175, F.218, I.221, F.230, R.235, L.238, G.266, S.267, A.268, G.269, Q.270, S.271, F.274, H.350, I.353, V.354, Y.357, I.358, L.388 Ligands: N39.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.130, A:Y.130, A:V.134, A:F.167, A:F.167, A:I.221, A:I.353, A:Y.357 Salt bridges: A:H.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, C. et al., Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype. Angew.Chem.Int.Ed.Engl. (2022)

Release Date

2022-08-24

Peptides

Indoleamine 2,3-dioxygenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Indoleamine 2,3-dioxygenase 1