SMTL ID : 9ife.2 (1 other biounit)

PANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z943693514

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 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 32 PLIP interactions: 30 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.54, 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:G.53, A:T.54, 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, B:H.464 Water bridges: A:G.16, A:S.17, A:A.49, A:G.52, A:G.164, A:S.165, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.9: 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 35 PLIP interactions: 33 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:C.55, B:K.63, B:G.130, B:G.130, B:G.164, B:R.293, B:D.330, B:M.336, B:T.338, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:S.17, B:A.49, B:G.52, B:T.54, B:S.165, B:I.331, B:A.341, A:H.464 pi-Stacking: B:F.201, B:F.201

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 4 residues within 4Å: Chain A: A.80, W.84, E.85, F.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.86, A:G.88 Water bridges: A:F.86 IMD.7: 5 residues within 4Å: Chain A: I.291, P.292, R.293, T.294, N.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.294, A:N.295 IMD.8: 4 residues within 4Å: Chain A: R.77, A.247, N.248, Y.411 No protein-ligand interaction detected (PLIP) IMD.10: 4 residues within 4Å: Chain B: R.77, A.247, N.248, Y.411 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.248

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

PEG.3: 5 residues within 4Å: Chain A: W.166, M.169, E.176, S.180, E.183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.166, A:E.176, A:S.180 Water bridges: A:N.182 PEG.4: 6 residues within 4Å: Chain A: A.386, K.387, F.389, E.390, K.483, G.484 No protein-ligand interaction detected (PLIP) PEG.5: 8 residues within 4Å: Chain A: P.167, S.181, F.201, I.202, A.287, I.288, G.289, R.290 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.181, A:F.201, A:I.202, A:G.289, A:R.290 Water bridges: A:S.181, A:G.200, A:S.203, A:I.288 PEG.6: 10 residues within 4Å: Chain A: V.197, G.198, G.199, C.223, Y.224, R.225, E.256, N.257, P.258, I.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.199, A:G.200, A:N.257 PEG.11: 6 residues within 4Å: Chain B: W.166, M.169, I.175, C.178, S.180, E.183 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.166, B:I.175, B:S.180 Water bridges: B:N.182

1 x GT4: ~{N}-(4-hydroxyphenyl)-2-methoxy-ethanamide(Non-covalent)

GT4.12: 6 residues within 4Å: Chain B: I.109, S.112, Y.113, G.115, M.116, D.119 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:M.116 Hydrogen bonds: B:S.112, B:D.119

2 x BR: BROMIDE ION(Non-functional Binders)(Non-covalent)

BR.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP BR.14: 3 residues within 4Å: Chain B: G.198, Y.224, R.225 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Exertier, C. et al., Expanding the molecular landscape of fragments binding to trypanothione reductase, a legitimate target for drug design against human African trypanosomiasis. Front Chem Biol (2025)

Release Date

2025-11-12

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Trypanothione reductase

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