SMTL ID : 8vzv.1

Human TDO (hTDO) in complex with LM10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM.1: 23 residues within 4Å: Chain A: 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, Y.334, L.335, T.338 Chain B: Y.26 Ligands: 01.3 14 PLIP interactions: 13 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.56, A:Y.63, A:F.67, A:F.124, A:F.137, A:F.142, A:W.308, A:M.319, A:L.335 Hydrogen bonds: A:S.135, A:R.309 Salt bridges: A:R.143 Metal complexes: A:H.312, H2O.1 HEM.4: 25 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, Y.159, W.308, R.309, H.312, M.315, V.316, M.319, G.325, Y.334, L.335, T.338 Ligands: 01.6 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions, 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.142, B:W.308, B:M.319, B:L.335 Hydrogen bonds: B:S.135, B:Y.159, B:Y.159, B:R.309, B:Y.334 Water bridges: B:R.143, B:R.156, B:T.338 Salt bridges: B:R.143 Metal complexes: B:H.312, H2O.2 HEM.7: 21 residues within 4Å: Chain C: 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, Y.334, L.335 Chain D: Y.26 20 PLIP interactions: 19 interactions with chain C, 1 Ligand-Water interactions, Hydrophobic interactions: C:F.56, 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:V.316, C:M.319, C:L.335 Hydrogen bonds: C:S.135, C:Y.334 Water bridges: C:R.309 Salt bridges: C:R.143, C:R.309 pi-Stacking: C:H.312 Metal complexes: C:H.312, H2O.5 HEM.9: 24 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, Y.334, L.335, T.338 Ligands: 01.11 19 PLIP interactions: 18 interactions with chain D, 1 Ligand-Water interactions, Hydrophobic interactions: D:F.56, D:Y.63, D:Y.63, D:Y.63, D:F.67, D:F.124, D:F.137, D:F.142, D:V.316, D:M.319, D:L.335, D:L.335 Hydrogen bonds: D:S.135, D:Y.159, D:R.309 Water bridges: D:R.143 Salt bridges: D:R.143 Metal complexes: D:H.312, H2O.6

4 x ZIQ: alpha-methyl-L-tryptophan

ZIQ.2: 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.5: 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.8: 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 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.192, 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.10: 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 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.192, D:P.197, D:I.279, D:F.288, D:P.291 Hydrogen bonds: D:E.89, D:W.192 Water bridges: D:V.86, D:W.192 Salt bridges: D:R.87, D:R.195

3 x 01: 6-fluoro-3-[(E)-2-(1H-tetrazol-5-yl)ethenyl]-1H-indole

01.3: 11 residues within 4Å: Chain A: F.56, H.60, R.128, L.131, A.134, S.135, G.136, L.320 Chain B: Y.26, Y.29 Ligands: HEM.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.131, A:A.134, B:Y.26, B:Y.29 Hydrogen bonds: A:R.128, A:G.136 pi-Stacking: A:F.56, A:F.56 01.6: 11 residues within 4Å: Chain A: Y.26, Y.29 Chain B: F.56, H.60, R.128, L.131, A.134, S.135, L.320, G.325 Ligands: HEM.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.131, B:A.134, A:Y.26 Hydrogen bonds: B:R.128 pi-Stacking: B:F.56, B:F.56 01.11: 10 residues within 4Å: Chain C: Y.26, Y.29, L.30 Chain D: F.56, H.60, R.128, A.134, S.135, L.320 Ligands: HEM.9 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.26, C:Y.29, D:A.134 Hydrogen bonds: D:R.128 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

2024-08-28

Peptides

Tryptophan 2,3-dioxygenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

D
DDD

Tryptophan 2,3-dioxygenase

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