SMTL ID : 8pf5.1 (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: 37 residues within 4Å: Chain A: I.12, G.13, G.15, S.16, G.17, 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.463, P.464 27 PLIP interactions: 26 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:V.38, A:A.48, A:G.52, 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, A:T.337, B:H.463 Water bridges: A:G.15, A:T.53, A:D.295, A:D.295 pi-Stacking: A:F.200, A:F.200 FAD.5: 36 residues within 4Å: Chain A: H.463, P.464 Chain B: I.12, G.13, G.15, S.16, G.17, 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, F.200, I.201, R.289, R.292, G.328, D.329, M.335, L.336, T.337, P.338, A.340 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.53, B:I.201, B:I.201 Hydrogen bonds: B:S.16, B:S.16, B:G.17, B:G.18, B:V.38, B:A.48, B:G.52, B:T.53, B:T.53, B:C.54, B:K.62, B:G.129, B:G.129, B:R.292, B:D.329, B:M.335, B:T.337, B:T.337, A:H.463 Water bridges: B:G.15, B:G.163, B:S.164, B:I.330, B:A.340 pi-Stacking: B:F.200, B:F.200

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: 19 residues within 4Å: Chain A: F.398, T.399, P.400, L.401, H.463, P.464, T.465, S.466, E.468, E.469, S.472 Chain B: E.20, V.55, V.60, K.63, L.64, I.108, Y.112 Ligands: PEG.7 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.401, A:L.401, A:P.464, B:K.63, B:L.64 Hydrogen bonds: A:L.401 Water bridges: A:M.402 Salt bridges: A:E.468, A:E.469 pi-Stacking: A:F.398 YJK.6: 13 residues within 4Å: Chain A: E.20, W.23, V.60, K.63, L.64 Chain B: F.398, T.399, P.400, L.401, P.464, T.465, S.466, E.469 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.401, B:P.464, A:W.23, A:K.63 Hydrogen bonds: B:L.401 pi-Stacking: B:F.398 Halogen bonds: A:V.60

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

PEG.3: 9 residues within 4Å: Chain A: P.166, G.199, F.200, I.201, M.285, A.286, I.287, G.288, R.289 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.201, A:G.288 Water bridges: A:S.180, A:S.180, A:I.287 PEG.7: 2 residues within 4Å: Chain B: S.111 Ligands: YJK.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.111

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

DMS.4: 11 residues within 4Å: Chain A: E.315, F.316, S.317, I.327, E.343, A.346, L.347, T.350, R.357, K.358, T.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.350

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
A

B
B

Trypanothione reductase

Trypanothione reductase

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