SMTL ID : 6gcp.1

Trypanosoma brucei PTR1 in complex with inhibitor 2d (F186)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: 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: EUK.2 29 PLIP interactions: 29 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.30, A:K.33, A:K.33, A:R.34, A:G.36, A:N.113 Salt bridges: A:K.33, A:R.34, A:R.34 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: EUK.5 27 PLIP interactions: 27 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:G.36, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 NAP.10: 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: EUK.11 23 PLIP interactions: 23 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:A.32, C:G.36, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.13: 28 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, A.116, T.146, L.179, C.180, D.181, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: EUK.14 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:P.224 Hydrogen bonds: D:R.34, D:I.35, D:H.55, 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:G.30, D:G.36, D:N.113 Salt bridges: D:R.34, D:R.34

4 x EUK: 6-[(3,4-dichlorophenyl)methylsulfanyl]-1,3-benzothiazol-2-amine(Non-covalent)

EUK.2: 12 residues within 4Å: Chain A: S.115, F.117, D.181, C.188, F.191, Y.194, V.226, L.229, P.230, M.233, W.241 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.230, A:W.241 Hydrogen bonds: A:S.115, A:Y.194 Water bridges: A:F.117 pi-Stacking: A:F.117, A:F.117, A:F.117 EUK.5: 11 residues within 4Å: Chain B: S.115, F.117, D.181, C.188, F.191, Y.194, V.226, P.230, M.233, W.241 Ligands: NAP.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.241 Hydrogen bonds: B:S.115, B:Y.194 Water bridges: B:F.117 pi-Stacking: B:F.117, B:F.117, B:F.117 EUK.11: 10 residues within 4Å: Chain C: S.115, F.117, D.181, C.188, Y.194, L.229, P.230, M.233, W.241 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.117, C:P.230, C:W.241 Hydrogen bonds: C:S.115 Water bridges: C:F.117 pi-Stacking: C:F.117, C:F.117 EUK.14: 10 residues within 4Å: Chain D: S.115, F.117, D.181, C.188, F.191, Y.194, P.230, M.233, W.241 Ligands: NAP.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.117, D:F.117, D:P.230, D:W.241 Hydrogen bonds: D:S.115 Water bridges: D:F.117 pi-Stacking: D:F.117, D:F.117

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: L.228, R.250, E.251, S.253 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.250, A:E.251 Water bridges: A:R.250, A:E.251, A:S.253 GOL.8: 5 residues within 4Å: Chain B: H.44, Q.45, E.67, L.68, E.71 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.44, B:Q.45, B:E.67, B:E.67 Water bridges: B:E.71, B:E.71 GOL.9: 3 residues within 4Å: Chain B: L.228, E.251, S.253 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.251, B:S.253, B:A.254 GOL.12: 4 residues within 4Å: Chain C: Y.54, V.78, C.79, Q.80 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.54, C:Q.80 Water bridges: C:R.102, C:R.102

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

ACT.6: 2 residues within 4Å: Chain B: Y.54, V.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.54, B:Y.54 ACT.7: 4 residues within 4Å: Chain B: A.232, M.233, G.234, E.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.235 Water bridges: B:K.238, B:K.238 Salt bridges: B:K.238

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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