SMTL ID : 7zv3.1

Crystal structure of indoleamine 2,3-dioxygenase 1 (IDO1) in complex with ferric heme and MMG-0472

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: F.183, S.187, V.190, F.234, I.237, F.246, S.283, A.284, G.285, F.290, R.363, H.366, I.369, V.370, Y.373, I.374, L.404, F.407, L.408, V.411 Ligands: RCT.2 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:F.183, A:V.190, A:F.234, A:F.234, A:I.237, A:F.246, A:F.290, A:I.369, A:V.370, A:Y.373, A:Y.373, A:L.404, A:F.407, A:F.407, A:L.408, A:L.408 Salt bridges: A:R.363 Metal complexes: A:H.366 HEM.5: 21 residues within 4Å: Chain B: Y.146, F.183, S.187, F.234, I.237, F.246, S.283, A.284, G.285, F.290, R.363, H.366, I.369, V.370, Y.373, I.374, L.404, F.407, L.408, V.411 Ligands: RCT.6 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:F.183, B:F.234, B:F.234, B:I.237, B:F.246, B:A.284, B:F.290, B:I.369, B:V.370, B:Y.373, B:I.374, B:F.407, B:L.408 Salt bridges: B:R.363 Metal complexes: B:H.366

2 x RCT: 4-(3-chloro-2-phenethylphenyl)-1H-1,2,3-triazole(Non-covalent)

RCT.2: 13 residues within 4Å: Chain A: Y.146, C.149, V.150, F.183, S.187, F.246, R.251, L.254, G.282, S.283, A.284, I.374 Ligands: HEM.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.146, A:Y.146, A:V.150, A:F.183, A:F.183, A:F.246, A:R.251, A:L.254, A:A.284, A:I.374 Hydrogen bonds: A:S.283, A:A.284 RCT.6: 11 residues within 4Å: Chain B: Y.146, C.149, V.150, F.183, S.187, R.251, L.254, G.282, S.283, A.284 Ligands: HEM.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.146, B:Y.146, B:V.150, B:F.183, B:F.183, B:R.251, B:L.254 Hydrogen bonds: B:S.283, B:A.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: G.306, H.307, A.308, A.309, T.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.307, A:A.308, A:A.309

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: W.273, E.274, D.275, K.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.274, A:D.275, A:D.275 Salt bridges: A:K.277 SO4.7: 4 residues within 4Å: Chain B: G.306, H.307, A.308, T.410 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.307, B:H.307, B:A.308, B:T.410 Water bridges: B:G.306, B:A.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohrig, U.F. et al., Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. J Enzyme Inhib Med Chem (2022)

Release Date

2022-07-06

Peptides

Indoleamine 2,3-dioxygenase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Indoleamine 2,3-dioxygenase 1

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