SMTL ID : 8w1h.1

Crystal Structure of human Tryptophan 2,3-dioxygenase in complex with PYN3 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: F.56, H.60, Y.63, 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 Chain B: Y.26 Ligands: 01.3 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:F.56, A:Y.63, A:Y.63, A:Y.63, A:L.116, A:F.124, A:F.124, A:F.142, A:Y.159, A:W.308, A:W.308, A:V.316, A:V.316, A:L.320, A:L.335, A:L.335 Hydrogen bonds: A:S.135, A:Y.159, A:Y.159, A:R.309 Water bridges: A:T.338 Salt bridges: A:R.143 pi-Cation interactions: A:H.60 Metal complexes: A:H.312 HEM.4: 24 residues within 4Å: Chain A: Y.26 Chain B: F.56, H.60, Y.63, 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: 01.6 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:F.56, B:Y.63, B:Y.63, B:Y.63, B:L.116, B:F.124, B:F.142, B:Y.159, B:W.308, B:W.308, B:V.316, B:M.319, B:L.320, B:L.335, B:L.335 Hydrogen bonds: B:Y.159, B:Y.159, B:R.309, B:Y.334 Salt bridges: B:R.143 pi-Cation interactions: B:H.60 Metal complexes: B:H.312 HEM.7: 22 residues within 4Å: Chain C: F.56, H.60, Y.63, 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, Y.334, L.335 Chain D: Y.26 Ligands: 01.9 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:F.56, C:Y.63, C:Y.63, C:Y.63, C:L.116, C:F.124, C:F.142, C:Y.159, C:W.308, C:W.308, C:V.316, C:L.335 Hydrogen bonds: C:S.135, C:Y.159, C:R.309, C:Y.334 Salt bridges: C:R.143 pi-Cation interactions: C:H.60 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: 01.12 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:F.56, D:Y.63, D:Y.63, D:Y.63, D:F.67, D:L.116, D:F.124, D:F.137, D:F.142, D:W.308, D:W.308, D:V.316, D:V.316, D:L.320, D:L.320, D:L.335 Hydrogen bonds: D:S.135, D:Y.159, D:R.309 Salt bridges: D:R.143 Metal complexes: D:H.312

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

ZIQ.2: 11 residues within 4Å: Chain A: V.86, 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:V.86, A:E.89, A:W.192 Salt bridges: A:R.87, A:R.195 ZIQ.5: 11 residues within 4Å: Chain B: V.86, 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.8: 11 residues within 4Å: Chain C: V.86, 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 C Hydrophobic interactions: C:W.192, 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.11: 11 residues within 4Å: Chain D: V.86, 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:V.86, D:E.89, D:W.192 Salt bridges: D:R.87, D:R.195

4 x 01: (6M)-1-[(imidazolidin-1-yl)methyl]-6-(1H-indol-3-yl)-1H-benzotriazole

01.3: 13 residues within 4Å: Chain A: F.56, H.60, F.124, R.128, L.131, S.132, P.133, A.134, G.136, L.320 Chain B: Y.26, Y.29 Ligands: HEM.1 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.26, B:Y.29, A:F.124, A:L.131, A:A.134, A:L.320 Hydrogen bonds: A:R.128, A:G.136 pi-Stacking: A:F.56, A:F.56 01.6: 13 residues within 4Å: Chain A: Y.26, Y.29 Chain B: F.56, H.60, F.124, R.128, S.132, P.133, A.134, S.135, G.136, L.320 Ligands: HEM.4 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.26, A:Y.29, B:F.124, B:A.134, B:L.320 Hydrogen bonds: B:G.136 pi-Stacking: B:F.56, B:F.56, B:H.60 01.9: 13 residues within 4Å: Chain C: F.56, H.60, F.124, R.128, S.132, P.133, A.134, S.135, G.136, L.320 Chain D: Y.26, Y.29 Ligands: HEM.7 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.124, C:A.134, C:L.320, D:Y.26, D:Y.29 Hydrogen bonds: C:R.128, C:G.136 pi-Stacking: C:F.56, C:F.56, C:H.60 01.12: 12 residues within 4Å: Chain C: Y.26, Y.29 Chain D: F.56, H.60, F.124, R.128, L.131, S.132, P.133, A.134, G.136 Ligands: HEM.10 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.124, D:L.131, D:A.134, C:Y.26, C:Y.29 Hydrogen bonds: D:R.128, D:G.136 pi-Stacking: D:F.56, D:F.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Geeraerts, Z. et al., Structural Insights into Protein-Inhibitor Interactions in Human Tryptophan Dioxygenase. J.Med.Chem. (2024)

Release Date

2024-08-21

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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