SMTL ID : 4nev.1

Crystal structure of Trypanothione Reductase from Trypanosoma brucei in complex with inhibitor EP127 (5-{5-[1-(PYRROLIDIN-1-YL)CYCLOHEXYL]-1,3-THIAZOL-2-YL}-1H-INDOLE)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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, S.181, F.201, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 Chain B: H.464, P.465 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.54, A:K.63 Hydrogen bonds: A:A.15, A:S.17, A:S.17, A:G.18, A:G.19, A:V.39, A:A.49, A:G.53, A:T.54, A:C.55, A:K.63, A:G.130, A:G.130, A:I.328, A:D.330, A:M.336, A:T.338, A:T.338, B:H.464 pi-Stacking: A:F.201, A:F.201 FAD.6: 36 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, R.290, R.293, G.329, D.330, M.336, L.337, T.338, P.339, A.341 25 PLIP interactions: 24 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:G.19, 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, A:H.464 Water bridges: B:A.49, B:G.164, B:G.164, B:S.165 pi-Stacking: B:F.201, B:F.201

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

2JR.2: 7 residues within 4Å: Chain A: L.20, E.21, W.24, S.112, Y.113, M.116, D.119 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.24, A:W.24, A:Y.113, A:M.116 Hydrogen bonds: A:D.119 Salt bridges: A:E.21 pi-Stacking: A:W.24 2JR.7: 7 residues within 4Å: Chain B: L.20, E.21, W.24, S.112, Y.113, G.115, M.116 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.20, B:W.24, B:W.24, B:M.116 Salt bridges: B:E.21 pi-Stacking: B:W.24 2JR.14: 5 residues within 4Å: Chain B: H.43, P.45, Y.48, Y.186, P.188 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.186, B:Y.186

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

SO4.3: 4 residues within 4Å: Chain A: G.200, F.201, G.289, R.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.201, A:R.290 Water bridges: A:G.200 SO4.4: 4 residues within 4Å: Chain A: Y.224, R.225, N.226, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.224 Salt bridges: A:R.225, A:R.231 SO4.5: 2 residues within 4Å: Chain A: K.260, S.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.262 Salt bridges: A:K.260 SO4.8: 3 residues within 4Å: Chain B: G.200, F.201, G.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.201, B:R.290 SO4.9: 2 residues within 4Å: Chain B: R.192, R.193 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.192, B:R.193 SO4.10: 3 residues within 4Å: Chain B: Y.458, N.459, R.475 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.458, B:Y.458, B:N.459 Salt bridges: B:R.475 SO4.11: 4 residues within 4Å: Chain A: Y.458, N.459, R.475 Chain B: R.358 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.459 Salt bridges: A:R.475, B:R.358 SO4.12: 2 residues within 4Å: Chain B: K.260, S.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.262, B:S.262 Salt bridges: B:K.260

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

EPE.13: 8 residues within 4Å: Chain B: F.47, W.129, T.143, A.144, W.166, R.293, N.295, D.296 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.144, B:R.293, B:N.295 Salt bridges: B:D.296, B:D.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Persch, E. et al., Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase. Chemmedchem (2014)

Release Date

2014-05-14

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase

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