SMTL ID : 7lu7.1

Human TDO (hTDO) in complex with NLG919 analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: F.56, T.59, H.60, Y.63, E.64, F.67, F.113, L.116, M.119, F.124, S.135, G.136, F.137, S.139, F.142, R.143, 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: 5PK.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:F.56, A:Y.63, A:Y.63, A:Y.63, A:F.67, A:F.124, A:F.137, A:F.137, A:F.142, A:W.308, A:W.308 Hydrogen bonds: A:G.136, A:R.309 Water bridges: A:R.143, A:R.156, A:T.338 Salt bridges: A:R.143 pi-Cation interactions: A:H.60 Metal complexes: A:H.312 HEM.5: 28 residues within 4Å: Chain A: Y.26 Chain B: F.56, T.59, H.60, Y.63, E.64, F.67, F.113, L.116, M.119, F.124, S.135, G.136, F.137, S.139, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, Y.334, L.335, T.338 Ligands: 5PK.4 18 PLIP interactions: 18 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:V.316, B:L.335 Hydrogen bonds: B:G.136 Water bridges: B:R.143, B:R.309 Salt bridges: B:R.143, B:R.309 Metal complexes: B:H.312 HEM.7: 29 residues within 4Å: Chain C: F.56, T.59, H.60, Y.63, E.64, F.67, F.113, L.116, M.119, F.124, S.135, G.136, F.137, S.139, F.142, R.143, W.308, R.309, H.312, M.315, V.316, M.319, L.320, Y.332, Y.334, L.335, T.338 Chain D: Y.26 Ligands: 5PK.9 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:F.56, C:Y.63, C:Y.63, C:Y.63, C:F.67, C:L.116, C:F.137, C:F.137, C:F.142, C:W.308, C:W.308, C:V.316, C:L.335 Hydrogen bonds: C:G.136 Water bridges: C:R.309, C:Y.332 Salt bridges: C:R.143, C:R.309 Metal complexes: C:H.312 HEM.10: 28 residues within 4Å: Chain C: Y.26 Chain D: F.56, T.59, H.60, Y.63, F.67, F.113, L.116, M.119, F.124, S.135, G.136, F.137, S.139, 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: 5PK.12 20 PLIP interactions: 20 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.137, D:F.137, D:F.142, D:W.308, D:W.308, D:V.316 Hydrogen bonds: D:G.136, D:F.137, D:R.309 Water bridges: D:R.143, D:R.143, D:T.338 Salt bridges: D:R.143 Metal complexes: D:H.312

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

ZIQ.2: 12 residues within 4Å: Chain A: V.86, R.87, E.89, W.192, L.193, R.195, T.196, P.197, I.279, R.287, F.288, P.291 11 PLIP interactions: 11 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:R.87, A:W.192 Water bridges: A:W.192 Salt bridges: A:R.87, A:R.195 ZIQ.6: 12 residues within 4Å: Chain B: V.86, R.87, E.89, W.192, L.193, R.195, T.196, P.197, I.279, R.287, F.288, P.291 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.192, B:P.197, B:I.279, B:F.288, B:P.291 Hydrogen bonds: B:R.87, B:W.192 Water bridges: B:W.192 Salt bridges: B:R.87, B:R.195 ZIQ.8: 12 residues within 4Å: Chain C: V.86, R.87, E.89, W.192, L.193, 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:P.197, C:F.288, C:F.288, C:P.291 Hydrogen bonds: C:E.89, C:E.89, C:W.192 Water bridges: C:W.192 Salt bridges: C:R.87, C:R.195 ZIQ.11: 12 residues within 4Å: Chain D: V.86, R.87, E.89, W.192, L.193, R.195, T.196, P.197, I.279, R.287, F.288, P.291 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.192, D:T.196, D:I.279, D:F.288, D:F.288, D:P.291 Hydrogen bonds: D:R.87, D:R.87, D:W.192 Water bridges: D:R.87, D:W.192 Salt bridges: D:R.87, D:R.195

4 x 5PK: (1~{R})-1-cyclohexyl-2-[(5~{S})-5~{H}-imidazo[1,5-b]isoindol-5-yl]ethanol(Non-covalent)

5PK.3: 15 residues within 4Å: Chain A: F.56, H.60, F.124, R.128, L.131, S.132, A.134, S.135, G.136, H.312, L.320 Chain B: Y.26, Y.29, L.30 Ligands: HEM.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.56, A:F.56, A:F.124, A:A.134, A:L.320, B:Y.26, B:Y.29 Hydrogen bonds: A:G.136, A:H.312 pi-Stacking: A:H.60 5PK.4: 15 residues within 4Å: Chain A: Y.26, Y.29, L.30 Chain B: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, H.312, L.320, K.323 Ligands: HEM.5 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.26, A:Y.29, B:F.124, B:A.134, B:L.320 Hydrogen bonds: B:H.312 pi-Stacking: B:F.56, B:H.60 5PK.9: 15 residues within 4Å: Chain C: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, H.312, L.320, Y.332 Chain D: Y.26, Y.29, L.30 Ligands: HEM.7 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.56, C:F.56, C:A.134, C:L.320, D:Y.26, D:Y.29 Hydrogen bonds: C:H.312 pi-Stacking: C:H.60 5PK.12: 14 residues within 4Å: Chain C: Y.26, Y.29, L.30 Chain D: F.56, H.60, F.124, R.128, L.131, A.134, S.135, G.136, H.312, L.320 Ligands: HEM.10 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.56, D:F.56, D:A.134, D:L.320, C:Y.26, C:Y.29 Hydrogen bonds: D:H.312 pi-Stacking: D:H.60

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

2022-08-24

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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