SMTL ID : 6oex.1

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor 3-(2-{1-[2-(Piperidin-4-yl)ethyl]-1H-indol-5-yl}-5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3- thiazol-4-yl)-N-(2,2,2-trifluoroethyl)prop-2-yn-1-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339 Chain B: H.464, P.465 31 PLIP interactions: 29 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:A.49, A:A.50, A:G.53, A:T.54, A:T.54, 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, B:H.464 Water bridges: A:G.16, A:A.49, A:G.164, A:G.164, A:S.165, A:S.165, A:A.341, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.6: 37 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, F.201, I.202, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 33 PLIP interactions: 31 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.54, B:I.202, B:I.202 Hydrogen bonds: B:A.15, B:S.17, B:S.17, B:G.18, B:G.19, B:V.39, B:A.49, B:G.53, B:T.54, B:T.54, B:C.55, B:K.63, B:G.130, B:G.130, B:D.330, B:M.336, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:A.49, B:T.54, B:S.165, B:D.296, B:D.296, B:I.331, B:A.341, A:H.464 pi-Stacking: B:F.201, B:F.201

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain A: W.129, T.143, A.144, W.166, R.293, D.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.144, A:R.293 Salt bridges: A:D.296, A:D.296 EPE.7: 11 residues within 4Å: Chain A: K.64 Chain B: F.399, P.401, L.402, P.465, T.466, S.467, E.469, E.470, S.473 Ligands: M9Y.5 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.402, B:P.465, B:S.473, B:S.473 Water bridges: B:S.397, B:M.403 Salt bridges: B:E.469, B:E.469, B:E.470, A:K.64

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: K.260, S.262, H.270 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.262, A:S.262 Water bridges: A:S.262, A:T.272 Salt bridges: A:K.260, A:H.270 SO4.4: 2 residues within 4Å: Chain A: R.192, R.193 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.193 Salt bridges: A:R.192, A:R.193

2 x M9Y: 3-(2-{1-[2-(piperidin-4-yl)ethyl]-1H-indol-5-yl}-5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-4-yl)-N-(2,2,2-trifluoroethyl)prop-2-yn-1-amine(Non-covalent)

M9Y.5: 11 residues within 4Å: Chain A: L.20, W.24, V.56, I.109, S.112, Y.113, G.115, M.116, D.119 Chain B: L.402 Ligands: EPE.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.113, A:M.116 Salt bridges: A:E.21 M9Y.8: 9 residues within 4Å: Chain B: L.20, W.24, V.61, I.109, S.112, Y.113, G.115, M.116, D.119 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.24, B:M.116 Water bridges: B:S.112 Salt bridges: B:E.21 pi-Stacking: B:W.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Gasparo, R. et al., Targeting a Large Active Site: Structure-Based Design of Nanomolar Inhibitors of Trypanosoma brucei Trypanothione Reductase. Chemistry (2019)

Release Date

2019-07-31

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Trypanothione reductase

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