SMTL ID : 6oey.1

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor (+)-5-{5-[1-(Pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1-{[(2S)-pyrrolidin-2-yl]methyl}-1H-indole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 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, 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 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.8: 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 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:D.330, B:M.336, B:T.338, B:T.338, B:T.338, A:H.464 Water bridges: B:G.16, B:A.49, B:T.54, B:S.165, 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: 7 residues within 4Å: Chain A: F.47, W.129, T.143, A.144, W.166, R.293, D.296 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.143, A:A.144, A:R.293 Water bridges: A:N.295 Salt bridges: A:D.296, A:D.296 EPE.9: 10 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 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.402, B:T.466 Water bridges: B:M.403 Salt bridges: B:E.469, B:E.469, B:E.470, B:E.470, A:K.64

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

SO4.3: 4 residues within 4Å: Chain A: R.77, A.247, N.248, Y.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.411 Water bridges: A:R.77, A:N.248 Salt bridges: A:R.77 SO4.4: 5 residues within 4Å: Chain A: R.334, T.360, D.361, H.362, T.363 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.362 Water bridges: A:R.334, A:R.334, A:R.334, A:D.361 Salt bridges: A:R.334, A:H.362 SO4.10: 2 residues within 4Å: Chain B: R.192, R.193 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.192, B:R.192 Salt bridges: B:R.192, B:R.193

4 x M9S: 5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1-{[(2S)-pyrrolidin-2-yl]methyl}-1H-indole(Non-covalent)

M9S.5: 10 residues within 4Å: Chain A: L.20, E.21, W.24, S.112, Y.113, G.115, M.116, D.119, T.120 Ligands: M9S.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.20, A:W.24, A:Y.113, A:M.116 Salt bridges: A:E.21 pi-Stacking: A:W.24 M9S.6: 6 residues within 4Å: Chain A: S.42, H.43, P.45, Y.48, N.103, Y.186 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.45, A:Y.186, A:Y.186, A:Y.186 M9S.7: 4 residues within 4Å: Chain A: S.112, Y.113, T.120 Ligands: M9S.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.112 M9S.11: 8 residues within 4Å: Chain B: L.20, E.21, W.24, S.112, Y.113, G.115, M.116, D.119 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.20, B:W.24, 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

Related Entries With Identical Sequence