SMTL ID : 6gd4.1

Trypanosoma brucei PTR1 in complex with inhibitor 4c (F188)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 28 residues within 4Å: Chain A: G.30, K.33, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 6KT.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:H.55, A:N.56, A:N.56, A:S.57, A:D.82, A:L.83, A:T.84, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:Y.194, A:K.198, A:S.227, A:L.228 Water bridges: A:G.36, A:S.57, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.4: 27 residues within 4Å: Chain B: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 6KT.5 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, B:H.55, B:H.55, B:N.56, B:N.56, B:S.57, B:D.82, B:D.82, B:L.83, B:T.84, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:Y.194, B:K.198, B:S.227, B:L.228 Water bridges: B:A.32, B:A.32, B:G.36, B:N.113 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.7: 27 residues within 4Å: Chain C: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 6KT.8 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:R.34, C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:D.82, C:L.83, C:T.84, C:N.113, C:S.115, C:S.115, C:S.115, C:K.198, C:S.227, C:L.228 Water bridges: C:A.32, C:G.36, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.11: 27 residues within 4Å: Chain D: G.30, R.34, I.35, H.53, Y.54, H.55, N.56, S.57, A.81, D.82, L.83, T.84, N.113, A.114, S.115, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 6KT.12 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, D:N.56, D:N.56, D:S.57, D:D.82, D:D.82, D:L.83, D:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:K.198, D:S.227, D:L.228 Water bridges: D:A.32, D:G.36, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x 6KT: 2-amino-1,3-benzothiazole-6-carboxamide(Non-covalent)

6KT.2: 7 residues within 4Å: Chain A: S.115, F.117, D.181, Y.194, G.225, V.226 Ligands: NAP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.115, A:S.115, A:Y.194 Water bridges: A:F.117 pi-Stacking: A:F.117, A:F.117 6KT.5: 6 residues within 4Å: Chain B: S.115, F.117, D.181, Y.194, G.225 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.115, B:S.115, B:Y.194 Water bridges: B:F.117 pi-Stacking: B:F.117, B:F.117 6KT.8: 7 residues within 4Å: Chain C: S.115, F.117, D.181, Y.194, G.225, P.230 Ligands: NAP.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.115 Water bridges: C:F.117 pi-Stacking: C:F.117, C:F.117 6KT.12: 7 residues within 4Å: Chain D: S.115, F.117, D.181, Y.194, G.225, P.230 Ligands: NAP.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.115, D:S.115 Water bridges: D:F.117 pi-Stacking: D:F.117, D:F.117

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: K.33, R.34, R.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.34 ACT.6: 4 residues within 4Å: Chain B: Q.80, A.81, S.92, E.95 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.95

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain C: V.77, V.78 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.78, C:V.78 Water bridges: C:A.65, C:N.69, C:N.69 GOL.10: 4 residues within 4Å: Chain C: Y.54, V.78, C.79, Q.80 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.54, C:Q.80 Water bridges: C:R.102

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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