SMTL ID : 6btl.1

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor RD117 1-[2-(Piperazin-1-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: I.13, G.14, A.15, 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, I.202, R.290, R.293, L.297, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.54, A:K.63, A:I.202 Hydrogen bonds: A:G.14, A:A.15, 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:I.328, A:D.330, A:M.336, A:T.338, A:T.338, B:H.464 FAD.8: 35 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, R.290, R.293, I.328, G.329, D.330, M.336, L.337, T.338, P.339 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.54 Hydrogen bonds: B:S.17, B:S.17, B:G.18, 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:G.164, B:R.293, B:I.328, B:D.330, B:M.336, B:T.338, B:T.338, A:H.464 pi-Stacking: B:F.201, B:F.201 FAD.16: 38 residues within 4Å: Chain C: I.13, G.14, A.15, 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, I.202, R.290, R.293, L.297, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain D: H.464, P.465 26 PLIP interactions: 25 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.54, C:K.63, C:I.202 Hydrogen bonds: C:G.14, C:A.15, C:S.17, C:G.18, C:G.19, C:V.39, C:A.49, C:A.50, C:G.53, C:T.54, C:T.54, C:C.55, C:K.63, C:G.130, C:G.130, C:R.293, C:I.328, C:D.330, C:M.336, C:T.338, C:T.338, C:T.338, D:H.464 FAD.23: 35 residues within 4Å: Chain C: H.464, P.465 Chain D: 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, R.290, R.293, I.328, G.329, D.330, M.336, L.337, T.338, P.339 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:T.54 Hydrogen bonds: D:S.17, D:S.17, D:G.18, D:A.49, D:A.50, D:G.53, D:T.54, D:C.55, D:K.63, D:G.130, D:G.130, D:G.164, D:R.293, D:I.328, D:D.330, D:M.336, D:T.338, D:T.338, D:T.338, C:H.464 pi-Stacking: D:F.201, D:F.201

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

SO4.2: 4 residues within 4Å: Chain A: G.200, F.201, G.289, R.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.201, A:R.290 SO4.3: 4 residues within 4Å: Chain A: Y.224, R.225, N.226, R.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.224, A:Y.224, A:N.226 Salt bridges: A:R.225 SO4.4: 1 residues within 4Å: Chain A: K.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.262 Salt bridges: A:K.260 SO4.7: 4 residues within 4Å: Chain A: S.134, Q.155 Chain C: R.141, R.153 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.134, A:Q.155, A:Q.155, C:R.153 Salt bridges: C:R.141 SO4.9: 3 residues within 4Å: Chain B: K.260, S.262, H.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.262 Salt bridges: B:K.260, B:H.270 SO4.17: 4 residues within 4Å: Chain C: G.200, F.201, G.289, R.290 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.201, C:R.290 SO4.18: 4 residues within 4Å: Chain C: Y.224, R.225, N.226, R.231 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.224, C:N.226 Salt bridges: C:R.225 SO4.19: 1 residues within 4Å: Chain C: K.260 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.262 Salt bridges: C:K.260 SO4.22: 4 residues within 4Å: Chain A: R.141, R.153 Chain C: S.134, Q.155 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.134, C:Q.155, C:Q.155, A:R.153 Salt bridges: A:R.141 SO4.24: 3 residues within 4Å: Chain D: K.260, S.262, H.270 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.262 Salt bridges: D:K.260, D:H.270

4 x RD7: 1-[2-(piperazin-1-yl)ethyl]-5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole(Non-covalent)

RD7.5: 7 residues within 4Å: Chain A: L.20, W.24, S.112, Y.113, G.115, M.116, D.119 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.20, A:W.24, A:W.24, A:Y.113, A:M.116 Salt bridges: A:E.21, A:D.119 pi-Stacking: A:W.24 RD7.11: 7 residues within 4Å: Chain B: L.20, W.24, S.112, Y.113, G.115, M.116, D.119 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.20, B:W.24, B:Y.113 Salt bridges: B:E.21, B:D.119 pi-Stacking: B:W.24 RD7.20: 7 residues within 4Å: Chain C: L.20, W.24, S.112, Y.113, G.115, M.116, D.119 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.20, C:W.24, C:W.24, C:Y.113, C:M.116 Salt bridges: C:E.21, C:D.119 pi-Stacking: C:W.24 RD7.26: 7 residues within 4Å: Chain D: L.20, W.24, S.112, Y.113, G.115, M.116, D.119 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.20, D:W.24, D:Y.113 Salt bridges: D:E.21, D:D.119 pi-Stacking: D:W.24

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.455, Y.458, N.459, R.475 Chain B: R.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.459, A:R.475 GOL.13: 2 residues within 4Å: Chain B: R.192, R.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.192, B:R.193 GOL.14: 3 residues within 4Å: Chain B: Y.458, N.459, R.475 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.458, B:N.459, B:R.475 GOL.15: 6 residues within 4Å: Chain B: Y.224, N.226, N.227, L.228, R.231, R.238 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.227, B:L.228, B:R.231, B:R.231, B:R.238 GOL.21: 5 residues within 4Å: Chain C: S.455, Y.458, N.459, R.475 Chain D: R.358 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.458, C:N.459, C:R.475 GOL.28: 2 residues within 4Å: Chain D: R.192, R.193 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.192, D:R.193 GOL.29: 3 residues within 4Å: Chain D: Y.458, N.459, R.475 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.459, D:R.475 GOL.30: 6 residues within 4Å: Chain D: Y.224, N.226, N.227, L.228, R.231, R.238 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.227, D:L.228, D:R.231, D:R.231, D:R.238

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

EPE.10: 7 residues within 4Å: Chain B: W.129, T.143, A.144, W.166, R.293, N.295, D.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.144, B:R.293 Salt bridges: B:D.296, B:D.296 EPE.12: 9 residues within 4Å: Chain B: G.199, G.200, F.201, Y.224, R.225, N.226, R.231, I.288, G.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.224, B:R.225 Water bridges: B:G.289 EPE.25: 7 residues within 4Å: Chain D: W.129, T.143, A.144, W.166, R.293, N.295, D.296 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.144, D:R.293 Salt bridges: D:D.296, D:D.296 EPE.27: 9 residues within 4Å: Chain D: G.199, G.200, F.201, Y.224, R.225, N.226, R.231, I.288, G.289 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.225 Water bridges: D:G.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

De Gasparo, R. et al., Biological Evaluation and X-ray Co-crystal Structures of Cyclohexylpyrrolidine Ligands for Trypanothione Reductase, an Enzyme from the Redox Metabolism of Trypanosoma. ChemMedChem (2018)

Release Date

2018-06-06

Peptides

Trypanothione reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Trypanothione reductase

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