SMTL ID : 8pf4.1 (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: 36 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, 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 37 PLIP interactions: 35 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, 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:G.53, 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:S.17, A:A.49, A:G.52, A:T.54, A:G.164, A:G.164, A:S.165, A:S.165, A:D.296, A:D.296, A:A.341, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.11: 38 residues within 4Å: Chain A: H.464, P.465 Chain B: 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 36 PLIP interactions: 34 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:A.49, B:G.53, B:G.164, B:G.164, B:S.165, B:S.165, B:A.341, B:A.368, A:H.464 pi-Stacking: B:F.201

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.2: 17 residues within 4Å: Chain A: F.399, T.400, P.401, L.402, P.465, T.466, S.467, E.470 Chain B: W.24, V.61, K.64, L.65, I.109, S.112, Y.113, M.116 Ligands: PEG.7 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.402, A:L.402, A:P.465, B:W.24, B:K.64, B:Y.113, B:M.116 Hydrogen bonds: A:L.402 Water bridges: A:M.403, A:T.466, A:T.466 pi-Stacking: A:F.399 YIA.10: 16 residues within 4Å: Chain A: E.21, 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 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.402, B:L.402, B:P.465, A:W.24, A:K.64, A:Y.113 Hydrogen bonds: B:L.402 Water bridges: B:M.403 pi-Stacking: B:F.399, A:W.24, A:W.24

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

PEG.3: 1 residues within 4Å: Chain A: H.3 No protein-ligand interaction detected (PLIP) PEG.4: 6 residues within 4Å: Chain A: F.201, I.202, A.287, I.288, G.289, R.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.286 Water bridges: A:I.202, A:I.288 PEG.5: 6 residues within 4Å: Chain A: P.173, G.174, H.177, V.261, S.262, L.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.263, A:L.263 PEG.7: 5 residues within 4Å: Chain A: M.396, S.397, S.398, E.470 Ligands: YIA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.398 PEG.8: 6 residues within 4Å: Chain A: T.363, R.364, V.365, C.378, G.379, L.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.364, A:V.365, A:V.365, A:G.379 PEG.13: 7 residues within 4Å: Chain B: K.64, Q.71, F.370, P.374, D.435, G.436, P.438 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.64, B:Q.71, B:Q.71, B:D.435, B:D.435, B:G.436 PEG.14: 3 residues within 4Å: Chain B: Y.458, R.475, T.476 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.475 PEG.15: 5 residues within 4Å: Chain B: P.46, Y.48, W.166, E.183 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.183 PEG.17: 5 residues within 4Å: Chain B: W.166, P.167, Q.168, M.169, I.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.166, B:M.169 PEG.18: 4 residues within 4Å: Chain B: E.316, K.359, T.360, D.361 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.316 Water bridges: B:R.334, B:K.359, B:K.359, B:T.360 PEG.19: 4 residues within 4Å: Chain B: H.43, P.45, N.103, Y.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.103 Water bridges: B:H.43, B:H.43 PEG.20: 5 residues within 4Å: Chain B: W.129, W.166, R.293, D.296 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.293 PEG.21: 7 residues within 4Å: Chain B: K.92, A.93, N.94, W.95, K.96, E.189, P.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.92, B:W.95, B:K.96, B:K.96 PEG.22: 7 residues within 4Å: Chain B: G.198, G.199, G.200, Y.224, A.287, I.288, G.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.199, B:G.200

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 5 residues within 4Å: Chain A: A.386, K.387, F.389, E.390, K.483 No protein-ligand interaction detected (PLIP) IMD.12: 4 residues within 4Å: Chain B: Q.40, S.42, H.43, P.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.43 IMD.16: 4 residues within 4Å: Chain B: R.77, A.247, N.248, Y.411 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:R.77

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

DMS.9: 3 residues within 4Å: Chain A: A.80, W.84, F.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.86 pi-Cation interactions: A:F.86 DMS.23: 2 residues within 4Å: Chain B: A.27, E.121 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.121 DMS.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) DMS.25: 5 residues within 4Å: Chain B: A.386, F.389, E.390, K.483, G.484 No protein-ligand interaction detected (PLIP) DMS.26: 5 residues within 4Å: Chain B: A.80, W.84, E.85, F.86, G.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.86 Water bridges: B:G.88 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase

Related Entries With Identical Sequence