SMTL ID : 6rb5.1

Trypanothione reductase in complex with 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 37 residues within 4Å: Chain A: I.30, G.31, G.33, S.34, G.35, G.36, V.54, D.55, V.56, A.66, A.67, G.70, T.71, C.72, V.75, G.76, C.77, K.80, G.145, W.146, G.147, A.179, T.180, G.181, F.218, I.219, R.307, R.310, G.346, D.347, M.353, L.354, T.355, P.356, A.358 Chain B: H.481, P.482 34 PLIP interactions: 32 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.71, A:I.219, A:I.219 Hydrogen bonds: A:S.34, A:S.34, A:G.35, A:G.36, A:V.56, A:A.66, A:A.67, A:G.70, A:T.71, A:T.71, A:C.72, A:K.80, A:G.147, A:G.147, A:R.310, A:D.347, A:M.353, A:T.355, A:T.355, B:H.481 Water bridges: A:G.33, A:A.66, A:T.71, A:G.181, A:G.181, A:S.182, A:D.313, A:A.358, B:H.481 pi-Stacking: A:F.218, A:F.218 FAD.12: 36 residues within 4Å: Chain A: H.481, P.482 Chain B: I.30, G.31, G.33, S.34, G.35, V.54, D.55, V.56, A.66, A.67, G.70, T.71, C.72, V.75, G.76, C.77, K.80, G.145, W.146, G.147, A.179, T.180, G.181, F.218, I.219, R.307, R.310, G.346, D.347, M.353, L.354, T.355, P.356, A.358 35 PLIP interactions: 33 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.71, B:I.219, B:I.219 Hydrogen bonds: B:S.34, B:S.34, B:G.35, B:G.36, B:V.56, B:A.66, B:G.70, B:T.71, B:T.71, B:C.72, B:K.80, B:G.147, B:G.147, B:R.310, B:D.347, B:M.353, B:T.355, B:T.355, A:H.481 Water bridges: B:G.33, B:S.34, B:A.66, B:G.69, B:G.181, B:G.181, B:S.182, B:S.182, B:S.182, B:A.358, A:H.481 pi-Stacking: B:F.218, B:F.218

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

SO4.2: 3 residues within 4Å: Chain A: R.158, V.167, R.170 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.167 Salt bridges: A:R.158, A:R.170 SO4.3: 2 residues within 4Å: Chain A: R.209, R.210 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.209, A:R.210 SO4.4: 3 residues within 4Å: Chain A: D.332, R.336, T.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.332, A:D.332 Water bridges: A:D.332 Salt bridges: A:R.336 SO4.5: 3 residues within 4Å: Chain A: R.381, R.466, N.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.468, A:N.468 Salt bridges: A:R.381 SO4.6: 4 residues within 4Å: Chain A: Y.241, R.242, N.243, R.248 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.243 Water bridges: A:Y.241, A:R.248 Salt bridges: A:R.242, A:R.248 SO4.7: 4 residues within 4Å: Chain A: G.217, F.218, I.305, G.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.218 Water bridges: A:I.219, A:R.307 SO4.13: 2 residues within 4Å: Chain B: G.217, F.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.218 Water bridges: B:I.219, B:I.305, B:R.307 SO4.14: 2 residues within 4Å: Chain B: R.209, R.210 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.209, B:R.210 SO4.15: 4 residues within 4Å: Chain B: Y.241, R.242, N.243, R.248 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.241, B:Y.241, B:N.243 Water bridges: B:I.305 Salt bridges: B:R.242, B:R.248 SO4.16: 2 residues within 4Å: Chain B: R.248, R.255 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.249, B:R.255 Salt bridges: B:R.255

4 x JWZ: 4-(((3-(8-(2-((1R,2S,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl)ethyl)-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]decan-3-yl)propyl)(methyl)amino)methyl)-4-hydroxypiperidine-1-carboximidamide(Non-covalent)

JWZ.8: 9 residues within 4Å: Chain A: E.38, W.41, V.73, V.78, I.126, S.129, Y.130, M.133 Chain B: H.481 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.41, A:V.73, A:V.78, A:I.126, A:Y.130 Hydrogen bonds: A:S.129 Salt bridges: A:E.38 JWZ.9: 7 residues within 4Å: Chain A: L.93, R.94, G.105, S.106, V.108, K.109, P.233 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.93, A:R.94, A:K.109, A:P.233 pi-Cation interactions: A:K.109 JWZ.17: 9 residues within 4Å: Chain B: E.38, W.41, V.73, V.78, I.126, S.129, Y.130, G.132, M.133 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.41, B:V.73, B:V.78, B:I.126, B:I.126, B:Y.130, B:M.133 Hydrogen bonds: B:S.129 Salt bridges: B:E.38 JWZ.18: 5 residues within 4Å: Chain B: G.105, S.106, V.108, K.109, P.233 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.108, B:K.109, B:P.233 pi-Cation interactions: B:K.109

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: W.183, R.310, N.312, D.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.313 Water bridges: A:D.313 GOL.11: 5 residues within 4Å: Chain A: Y.241, N.243, N.244, L.245, R.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.241, A:N.244, A:L.245, A:R.255 GOL.19: 6 residues within 4Å: Chain B: H.379, T.380, R.381, V.382, C.395, G.396 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.382, B:V.382, B:G.396, B:G.396 Water bridges: B:R.381, B:R.381 GOL.20: 4 residues within 4Å: Chain B: S.490, M.491, R.492, T.493 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.492, B:T.493, B:T.493, B:T.493 GOL.21: 3 residues within 4Å: Chain B: R.158, V.167, R.170 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.158, B:R.158, B:R.170, B:R.170 Water bridges: B:V.167 GOL.22: 4 residues within 4Å: Chain A: K.81 Chain B: L.419, T.483, S.484 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.419 Water bridges: B:T.483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Turcano, L. et al., Spiro-containing derivatives show antiparasitic activity against Trypanosoma brucei through inhibition of the trypanothione reductase enzyme. Plos Negl Trop Dis (2020)

Release Date

2020-05-13

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase