SMTL ID : 5ebk.1

Trypanothione reductase in complex with 6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 39 residues within 4Å: Chain A: G.31, A.32, 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, F.146, G.147, A.179, T.180, G.181, S.198, Y.218, R.307, R.310, L.314, I.345, G.346, D.347, M.353, L.354, T.355, P.356, A.358 Chain B: H.481, P.482 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.71 Hydrogen bonds: A:G.31, A:A.32, A:S.34, A:S.34, A:G.35, A:G.36, A:V.56, A:A.66, A:G.70, A:T.71, A:C.72, A:K.80, A:G.147, A:G.147, A:G.181, A:I.345, A:D.347, A:M.353, A:T.355, A:T.355, A:T.355, B:H.481 pi-Stacking: A:Y.218 FAD.7: 37 residues within 4Å: Chain A: H.481, P.482 Chain B: G.31, A.32, 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.147, A.179, T.180, G.181, S.198, Y.218, R.307, R.310, L.314, I.345, G.346, D.347, M.353, L.354, T.355, P.356, A.358 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.71, B:K.80 Hydrogen bonds: B:A.32, 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:Y.218, B:D.347, B:M.353, B:T.355, B:T.355, A:H.481 pi-Stacking: B:Y.218

7 x RDS: 6-sec-Butoxy-2-[(3-chlorophenyl)sulfanyl]-4-pyrimidinamine(Non-covalent)

RDS.2: 13 residues within 4Å: Chain A: S.34, C.72, V.73, C.77, Y.130, T.355 Chain B: L.419, H.481, P.482, E.486, E.487, S.490 Ligands: RDS.6 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Halogen bonds: A:T.355 Hydrogen bonds: B:E.486, B:E.486 pi-Cation interactions: B:H.481 RDS.3: 5 residues within 4Å: Chain A: Y.241, R.242, R.248, N.274, I.305 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.241, A:R.242 Hydrogen bonds: A:R.242, A:N.274 pi-Cation interactions: A:R.242 RDS.4: 3 residues within 4Å: Chain A: R.242, D.244, N.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.272, A:N.272 RDS.6: 6 residues within 4Å: Chain B: S.415, F.416, T.417, L.419, E.487 Ligands: RDS.2 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.419, B:L.419 Halogen bonds: B:E.487 RDS.8: 12 residues within 4Å: Chain A: L.419, H.481, E.486, E.487, S.490 Chain B: S.34, C.72, V.73, C.77, V.78, Y.130, T.355 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.73, B:V.78 Hydrogen bonds: A:E.486 pi-Stacking: A:H.481 RDS.9: 7 residues within 4Å: Chain B: L.187, G.215, Y.241, R.242, R.248, N.274, I.305 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.187, B:Y.241, B:R.242, B:I.305 Hydrogen bonds: B:R.242, B:R.242, B:N.274 pi-Cation interactions: B:R.242 RDS.10: 3 residues within 4Å: Chain B: R.242, D.244, N.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.272, B:N.272

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

SO4.5: 6 residues within 4Å: Chain A: G.217, Y.218, I.219, A.304, I.305, G.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.219, A:A.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saccoliti, F. et al., Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives. J Enzyme Inhib Med Chem (2017)

Release Date

2016-10-26

Peptides

Trypanothione reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Trypanothione reductase

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