SMTL ID : 6pyz.1

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PF-06840003 in Active Site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 32 residues within 4Å: Chain A: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, N.160, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain B: Y.26 Ligands: H7S.2 28 PLIP interactions: 27 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.56, A:T.59, A:Y.63, A:Y.63, A:Y.63, A:F.67, A:F.124, A:F.137, A:F.142, A:W.308, A:M.319, A:L.320, A:L.335 Hydrogen bonds: A:S.135, A:N.160, A:R.309, A:G.325, A:G.327, A:G.328, A:S.329, A:S.329 Water bridges: A:R.143, A:Y.334, A:T.338 Salt bridges: A:R.143 pi-Stacking: A:H.312 Metal complexes: A:H.312, H2O.2 HEM.4: 30 residues within 4Å: Chain A: Y.26 Chain B: F.56, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Ligands: H7S.5 25 PLIP interactions: 25 interactions with chain B, Hydrophobic interactions: B:F.56, B:Y.63, B:Y.63, B:Y.63, B:F.67, B:F.124, B:F.137, B:F.137, B:F.142, B:W.308, B:M.319, B:L.335 Hydrogen bonds: B:S.135, B:R.309, B:G.325, B:G.327, B:G.328, B:S.329, B:S.329, B:Y.334 Water bridges: B:R.143, B:R.143 Salt bridges: B:R.143 pi-Stacking: B:H.312 Metal complexes: B:H.312 HEM.7: 31 residues within 4Å: Chain C: F.56, T.59, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, G.325, T.326, G.327, G.328, S.329, G.331, Y.334, L.335, T.338 Chain D: Y.26 Ligands: H7S.8 26 PLIP interactions: 26 interactions with chain C, Hydrophobic interactions: C:F.56, C:T.59, C:Y.63, C:Y.63, C:Y.63, C:F.67, C:F.124, C:F.137, C:F.142, C:W.308, C:M.319, C:L.320, C:L.335 Hydrogen bonds: C:S.135, C:R.309, C:G.325, C:G.327, C:G.328, C:S.329, C:S.329, C:Y.334 Water bridges: C:R.143, C:R.143 Salt bridges: C:R.143 pi-Stacking: C:H.312 Metal complexes: C:H.312 HEM.10: 25 residues within 4Å: Chain C: Y.26 Chain D: F.56, H.60, Y.63, F.67, L.116, M.119, F.124, S.135, G.136, F.137, F.142, R.143, Y.159, W.308, R.309, H.312, M.315, V.316, M.319, L.320, Y.334, L.335, T.338 Ligands: H7S.11 19 PLIP interactions: 19 interactions with chain D, Hydrophobic interactions: D:F.56, D:Y.63, D:Y.63, D:Y.63, D:F.67, D:F.124, D:F.124, D:F.137, D:F.142, D:M.319, D:L.320, D:L.335 Hydrogen bonds: D:S.135, D:Y.159, D:R.309 Water bridges: D:R.143, D:R.143 Salt bridges: D:R.143 Metal complexes: D:H.312

4 x H7S: (3S)-3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione(Non-covalent)

H7S.2: 14 residues within 4Å: Chain A: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, L.320, G.325, T.326 Chain B: Y.26, Y.29 Ligands: HEM.1 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.124, B:Y.26, B:Y.26, B:Y.29 Hydrogen bonds: A:H.60, A:R.128, A:G.136, A:T.326 pi-Stacking: A:F.56, A:F.56, A:H.60 H7S.5: 12 residues within 4Å: Chain A: Y.26, Y.29 Chain B: F.56, H.60, R.128, A.134, S.135, G.136, L.320, G.325, T.326 Ligands: HEM.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.134, B:T.326, A:Y.26, A:Y.26, A:Y.29 Hydrogen bonds: B:H.60, B:R.128, B:G.136, B:T.326 pi-Stacking: B:F.56, B:F.56, B:H.60 H7S.8: 12 residues within 4Å: Chain C: F.56, H.60, R.128, A.134, S.135, G.136, L.320, G.325, T.326 Chain D: Y.26, Y.29 Ligands: HEM.7 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:H.60, C:R.128, C:G.136, C:T.326 pi-Stacking: C:F.56, C:F.56, C:H.60 Hydrophobic interactions: D:Y.26, D:Y.26, D:Y.29 H7S.11: 9 residues within 4Å: Chain C: Y.26, Y.29 Chain D: F.56, H.60, A.134, S.135, G.136, L.320 Ligands: HEM.10 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:A.134, C:Y.26, C:Y.26, C:Y.29 Hydrogen bonds: D:H.60, D:G.136 pi-Stacking: D:F.56, D:F.56

4 x ZIQ: alpha-methyl-L-tryptophan(Non-covalent)

ZIQ.3: 10 residues within 4Å: Chain A: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.192, A:P.197, A:I.279, A:F.288, A:P.291 Hydrogen bonds: A:R.87, A:E.89, A:W.192 Salt bridges: A:R.87, A:R.195 ZIQ.6: 10 residues within 4Å: Chain B: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.192, B:P.197, B:I.279, B:F.288, B:P.291 Hydrogen bonds: B:E.89, B:W.192 Salt bridges: B:R.87, B:R.195 ZIQ.9: 10 residues within 4Å: Chain C: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.192, C:T.196, C:P.197, C:I.279, C:F.288, C:P.291 Hydrogen bonds: C:E.89, C:E.89, C:W.192 Salt bridges: C:R.87, C:R.195 ZIQ.12: 10 residues within 4Å: Chain D: R.87, E.89, W.192, R.195, T.196, P.197, I.279, R.287, F.288, P.291 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.192, D:P.197, D:I.279, D:F.288, D:P.291 Hydrogen bonds: D:R.87, D:E.89, D:W.192 Salt bridges: D:R.87, D:R.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pham, K.N. et al., Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J.Am.Chem.Soc. (2019)

Release Date

2020-01-01

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Tryptophan 2,3-dioxygenase

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