SMTL ID : 8pf4.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: I.13, G.14, G.16, S.17, G.18, G.19, 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, S.181, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, A:F.201, A:I.202, A:I.202 Hydrogen bonds: A:S.17, A:S.17, A:G.18, A:G.19, A:V.39, A:A.49, A:A.50, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:R.293, A:D.330, A:M.336, A:T.338, A:T.338, A:T.338, B:H.464 Water bridges: A:G.16, A:A.49, A:T.54, A:T.54, A:S.165, A:D.296, A:D.296, A:I.331, B:H.464 pi-Stacking: A:F.201 FAD.13: 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 34 PLIP interactions: 32 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.54, B:F.201, 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:S.17, B:G.52, B:G.164, B:S.165, B:S.165, B:S.165, B:A.341, A:H.464 pi-Stacking: B:F.201

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

PEG.2: 5 residues within 4Å: Chain A: A.80, W.84, E.85, F.86, G.88 No protein-ligand interaction detected (PLIP) PEG.3: 4 residues within 4Å: Chain A: N.94, K.96, K.97, A.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.94 PEG.4: 6 residues within 4Å: Chain A: D.108, I.109, S.112, M.116 Chain B: L.402 Ligands: YIA.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.105, A:S.112 PEG.5: 6 residues within 4Å: Chain A: H.464, E.469 Chain B: T.338, P.339, I.342 Ligands: YIA.12 No protein-ligand interaction detected (PLIP) PEG.6: 6 residues within 4Å: Chain A: W.166, P.167, Q.168, M.169, I.291 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.168, A:M.169 PEG.7: 5 residues within 4Å: Chain A: Q.168, M.169, P.170, I.288 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain A: R.192, R.193, D.266, D.282 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.192, A:R.193, A:D.282 Water bridges: A:R.192, A:D.266, A:D.266 PEG.10: 4 residues within 4Å: Chain A: D.315, R.319, T.320, N.321 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.315 PEG.11: 3 residues within 4Å: Chain A: K.97 Chain B: A.80, G.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.81 Water bridges: B:G.83 PEG.15: 5 residues within 4Å: Chain B: H.43, G.44, P.45, N.103 Ligands: DMS.21 No protein-ligand interaction detected (PLIP) PEG.16: 2 residues within 4Å: Chain B: A.247, G.249 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.247 PEG.17: 3 residues within 4Å: Chain A: S.90 Chain B: F.86, D.87 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.87, A:S.90 PEG.18: 7 residues within 4Å: Chain B: G.198, G.199, G.200, F.201, Y.224, A.287, I.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.199, B:F.201 Water bridges: B:R.225 PEG.19: 8 residues within 4Å: Chain A: P.465, T.466 Chain B: F.370, P.374, D.435, G.436, P.438, E.439 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:P.465, B:D.435, B:D.435, B:G.436, B:E.439 Water bridges: B:Q.71, B:Q.71 PEG.20: 5 residues within 4Å: Chain B: K.6, V.150, K.151, E.152, R.153 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.153 Water bridges: B:K.6, B:E.152

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 4 residues within 4Å: Chain A: P.292, R.293, T.294, N.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.294, A:N.295

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

YIA.12: 17 residues within 4Å: Chain A: F.399, T.400, P.401, L.402, P.465, T.466, E.470 Chain B: L.20, W.24, V.61, K.64, L.65, I.109, Y.113, M.116, L.123 Ligands: PEG.5 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.20, B:L.20, B:W.24, B:K.64, B:Y.113, B:Y.113, B:M.116, B:L.123, A:L.402, A:L.402, A:P.465 Halogen bonds: B:V.61 Hydrogen bonds: A:L.402 Water bridges: A:M.403 pi-Stacking: A:F.399 YIA.14: 17 residues within 4Å: Chain A: L.20, W.24, V.61, K.64, L.65, Y.113, M.116 Chain B: F.399, T.400, P.401, L.402, H.464, P.465, T.466, S.467, E.470 Ligands: PEG.4 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.402, B:P.465, A:L.20, A:L.20, A:W.24, A:K.64, A:Y.113, A:Y.113, A:M.116 Hydrogen bonds: B:L.402 Water bridges: B:M.403, B:T.466 pi-Stacking: B:F.399, A:Y.113

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

DMS.21: 6 residues within 4Å: Chain B: Q.40, S.42, H.43, P.45, P.46 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.41 DMS.22: 5 residues within 4Å: Chain B: A.80, W.84, E.85, F.86, G.88 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.86 pi-Cation interactions: B:F.86 DMS.23: 3 residues within 4Å: Chain B: T.254, E.256, K.277 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.277 Salt bridges: B:E.256

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
C

B
D

Trypanothione reductase

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