SMTL ID : 8pf5.2 (1 other biounit)

Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

hetero-1-1-mer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 38 residues within 4Å: Chain A: I.12, G.13, G.15, S.16, G.17, G.18, V.36, D.37, V.38, A.48, A.49, G.52, T.53, C.54, V.57, G.58, C.59, K.62, G.127, W.128, G.129, A.161, T.162, G.163, S.180, F.200, I.201, R.289, R.292, G.328, D.329, M.335, L.336, T.337, P.338, A.340 Chain B: H.464, P.465 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.53, A:I.201 Hydrogen bonds: A:S.16, A:S.16, A:G.17, A:G.18, A:A.48, A:A.49, A:T.53, A:T.53, A:T.53, A:C.54, A:K.62, A:G.129, A:G.129, A:R.292, A:D.329, A:M.335, A:T.337, A:T.337, B:H.464 Water bridges: A:S.164, A:S.164, A:I.330 pi-Stacking: A:F.200 FAD.5: 37 residues within 4Å: Chain A: H.463, P.464 Chain B: I.13, G.14, G.16, S.17, G.18, V.37, D.38, V.39, A.49, A.50, G.53, T.54, C.55, V.58, G.59, C.60, K.63, G.128, W.129, G.130, A.162, T.163, G.164, F.201, I.202, R.290, R.293, L.297, G.329, D.330, M.336, L.337, T.338, P.339, A.341 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.54, B:F.201, B:I.202, B:I.202 Hydrogen bonds: B:G.14, B:S.17, B:S.17, B:G.18, B:G.19, B:A.50, B:G.53, B:T.54, B:C.55, B:K.63, B:G.130, B:G.130, B:R.293, B:D.330, B:M.336, B:T.338, B:T.338, B:T.338, A:H.463 Water bridges: B:S.17, B:A.49, B:G.52, B:T.54, B:G.164, B:S.165, B:I.331 pi-Stacking: B:F.201

2 x YJK: 4-[(3,4-dichlorophenyl)methyl]-~{N}-[[5-[2-(4-fluorophenyl)ethylcarbamoyl]furan-2-yl]methyl]-4-(3-phenylpropyl)-1,4$l^{4}-diazinane-1-carboxamide(Non-covalent)

YJK.2: 17 residues within 4Å: Chain A: F.398, T.399, P.400, L.401, H.463, P.464, T.465, S.466, E.469, S.472 Chain B: E.21, V.61, K.64, L.65, I.109, Y.113, I.342 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.61, B:K.64, B:I.109, B:I.109, B:Y.113, A:F.398, A:P.464 Halogen bonds: B:V.61 Hydrogen bonds: A:L.401 pi-Stacking: A:F.398 YJK.6: 17 residues within 4Å: Chain A: L.19, E.20, W.23, V.60, K.63, L.64, I.108, Y.112 Chain B: F.399, T.400, P.401, L.402, H.464, P.465, T.466, S.467, E.470 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.19, A:W.23, A:W.23, A:K.63, B:F.399, B:L.402, B:P.465 Halogen bonds: A:V.60 Hydrogen bonds: B:L.402 Water bridges: B:T.466 pi-Stacking: B:F.399

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: P.166, S.179, S.180, I.201, M.285, A.286, I.287, G.288, R.289 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.180, A:S.180, A:G.288 Water bridges: A:G.199, A:A.286, A:I.287, A:I.287 PEG.4: 2 residues within 4Å: Chain A: R.192, D.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.192

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 5 residues within 4Å: Chain B: L.76, A.80, W.84, F.86, G.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.86 pi-Cation interactions: B:F.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Exertier, C. et al., Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis. J.Med.Chem. (2024)

Release Date

2024-04-03

Peptides

Trypanothione reductase: A
Trypanothione reductase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Trypanothione reductase

Trypanothione reductase

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