SMTL ID : 8pf3.1 (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)(4-fluorophenyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: 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, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 30 PLIP interactions: 28 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54 Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:V.39, A:A.49, A:G.53, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:D.330, A:M.336, A:T.338, A:T.338, A:T.338, B:H.464 Water bridges: A:G.16, A:G.19, A:A.49, A:T.54, A:G.164, A:S.165, A:S.165, A:A.341, A:A.368, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.5: 36 residues within 4Å: Chain A: H.464, P.465 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, G.329, D.330, M.336, L.337, T.338, P.339, A.341 32 PLIP interactions: 30 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.54, B:I.202, B:I.202 Hydrogen bonds: B:S.17, B:S.17, B:G.18, B:G.19, B:V.39, B:A.49, B:A.50, B:G.53, B:T.54, 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, A:H.464 Water bridges: B:G.16, B:G.164, B:S.165, B:S.165, B:I.331, B:A.341, A:H.464 pi-Stacking: B:F.201, B:F.201

2 x YJ6: 4-[(3,4-dichlorophenyl)methyl]-~{N}-(4-fluorophenyl)-~{N}-[[5-[2-(4-fluorophenyl)ethylcarbamoyl]furan-2-yl]methyl]-4-(3-phenylpropyl)-1,4$l^{4}-diazinane-1-carboxamide(Non-covalent)

YJ6.2: 14 residues within 4Å: Chain A: S.397, F.399, P.401, L.402, H.464, P.465, T.466, S.467, E.469, E.470 Chain B: E.21, V.61, K.64, L.65 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.399, A:F.399, A:P.465, A:E.469, B:K.64 Hydrogen bonds: A:S.397, A:L.402 Water bridges: A:M.403, A:T.466 Salt bridges: A:E.470 pi-Cation interactions: A:H.464 Halogen bonds: B:V.61 YJ6.6: 16 residues within 4Å: Chain A: E.21, V.61, K.64, L.65, T.338, P.339, I.342 Chain B: F.399, P.401, L.402, H.464, P.465, T.466, E.469, E.470, S.473 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.465, A:K.64, A:I.342 Hydrogen bonds: B:L.402 Water bridges: B:M.403 Salt bridges: B:E.470 pi-Stacking: B:F.399 Halogen bonds: A:V.61

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

PEG.3: 7 residues within 4Å: Chain A: V.39, F.47, L.127, G.128, W.129, E.142, K.151 No protein-ligand interaction detected (PLIP) PEG.4: 5 residues within 4Å: Chain A: G.200, F.201, I.202, S.203, A.287 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.200, A:F.201, A:I.202, A:S.203, A:A.287

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 7 residues within 4Å: Chain B: V.314, D.315, S.318, T.332, R.334, E.344, H.362 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.332, B:R.334, B:E.344 pi-Cation interactions: B:H.362

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase

Related Entries With Identical Sequence