SMTL ID : 6gck.1

Trypanosoma brucei PTR1 in complex with inhibitor 1e (F206)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 27 residues within 4Å: Chain A: G.10, K.13, R.14, I.15, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: EUB.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.204 Hydrogen bonds: A:R.14, A:I.15, A:H.35, A:H.35, A:N.36, A:N.36, A:S.37, A:L.63, A:T.64, A:T.64, A:T.64, A:N.93, A:S.95, A:S.95, A:S.95, A:Y.174, A:K.178, A:S.207, A:L.208 Water bridges: A:K.13, A:K.13, A:G.16, A:N.93 Salt bridges: A:K.13, A:R.14, A:R.14 pi-Stacking: A:H.35 NAP.3: 27 residues within 4Å: Chain B: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: EUB.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.14, B:I.15, B:H.35, B:H.35, B:N.36, B:N.36, B:S.37, B:D.62, B:L.63, B:T.64, B:T.64, B:T.64, B:N.93, B:S.95, B:S.95, B:S.95, B:Y.174, B:K.178, B:S.207, B:L.208 Water bridges: B:G.16, B:N.93 Salt bridges: B:R.14, B:R.14 pi-Stacking: B:H.35 NAP.6: 28 residues within 4Å: Chain C: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, A.96, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: EUB.7 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.204 Hydrogen bonds: C:R.14, C:I.15, C:H.35, C:N.36, C:N.36, C:S.37, C:L.63, C:T.64, C:T.64, C:N.93, C:S.95, C:S.95, C:S.95, C:K.178, C:S.207, C:L.208 Water bridges: C:A.12, C:G.16, C:N.93 Salt bridges: C:R.14, C:R.14 NAP.8: 27 residues within 4Å: Chain D: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: EUB.9 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: D:R.14, D:I.15, D:H.35, D:N.36, D:N.36, D:S.37, D:D.62, D:D.62, D:L.63, D:T.64, D:N.93, D:S.95, D:S.95, D:S.95, D:K.178, D:S.207, D:L.208 Water bridges: D:G.10, D:G.16, D:T.64, D:N.93 Salt bridges: D:R.14, D:R.14 pi-Stacking: D:H.35

4 x EUB: 4-[(2-azanyl-1,3-benzothiazol-6-yl)oxymethyl]benzenecarbonitrile(Non-covalent)

EUB.2: 11 residues within 4Å: Chain A: S.95, F.97, D.161, C.168, Y.174, V.206, P.210, M.213, E.217, W.221 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.210, A:W.221 Hydrogen bonds: A:S.95, A:Y.174 Water bridges: A:E.217 pi-Stacking: A:F.97, A:F.97, A:F.97 EUB.4: 9 residues within 4Å: Chain B: S.95, F.97, D.161, C.168, F.171, Y.174, M.213, W.221 Ligands: NAP.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.95, B:Y.174 pi-Stacking: B:F.97, B:F.97, B:F.97, B:W.221, B:W.221 EUB.7: 10 residues within 4Å: Chain C: S.95, F.97, D.161, C.168, F.171, Y.174, P.210, M.213, W.221 Ligands: NAP.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.97, C:P.210, C:W.221 Hydrogen bonds: C:S.95, C:S.95 Water bridges: C:F.97 pi-Stacking: C:F.97, C:F.97 EUB.9: 11 residues within 4Å: Chain D: S.95, F.97, D.161, C.168, F.171, Y.174, V.206, P.210, M.213, W.221 Ligands: NAP.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.97, D:F.97, D:P.210, D:W.221 Hydrogen bonds: D:S.95 pi-Stacking: D:F.97, D:F.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain B: Y.34, V.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.34 Water bridges: B:V.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linciano, P. et al., Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections. J.Med.Chem. (2019)

Release Date

2019-04-03

Peptides

Pteridine reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase

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