SMTL ID : 5jcx.1

Trypanosoma brucei PTR1 in complex with inhibitor NP-29

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: 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: CC6.2 26 PLIP interactions: 26 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:G.36, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.6: 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: CC6.7 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:P.224 Hydrogen bonds: B:R.34, B:I.35, 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:G.30, B:G.36, B:H.55, B:H.55, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.10: 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: CC6.11 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:G.30, D:G.36, D:N.113, D:S.115, D:N.147 Salt bridges: D:R.34, D:R.34

3 x CC6: 3,5,7-trihydroxy-2-(2-hydroxyphenyl)-4H-1-benzopyran-4-one(Non-covalent)

CC6.2: 11 residues within 4Å: Chain A: R.34, F.117, D.181, C.188, Y.194, G.225, V.226, P.230, M.233, W.241 Ligands: NAP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.117 Hydrogen bonds: A:R.34, A:Y.194, A:Y.194, A:G.225 Water bridges: A:D.181, A:D.181 pi-Stacking: A:F.117, A:F.117, A:W.241, A:W.241 CC6.7: 10 residues within 4Å: Chain B: R.34, F.117, D.181, C.188, Y.194, L.229, P.230, M.233, W.241 Ligands: NAP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.117, B:L.229, B:P.230 Hydrogen bonds: B:R.34, B:Y.194, B:Y.194, B:G.225 Water bridges: B:D.181, B:G.225 pi-Stacking: B:F.117, B:F.117, B:W.241, B:W.241 CC6.11: 11 residues within 4Å: Chain D: R.34, F.117, D.181, Y.194, G.225, V.226, L.229, P.230, M.233, W.241 Ligands: NAP.10 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.117, D:V.226, D:L.229, D:P.230 Hydrogen bonds: D:R.34, D:Y.194, D:G.225 Water bridges: D:D.181, D:D.181, D:Y.194 pi-Stacking: D:F.117, D:F.117, D:W.241, D:W.241

5 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.4: 4 residues within 4Å: Chain A: I.262, F.263, S.266, S.268 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:F.263, B:S.268 ACT.8: 2 residues within 4Å: Chain C: V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78 Water bridges: C:N.69 ACT.9: 4 residues within 4Å: Chain C: Y.54, V.78, C.79, Q.80 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.80 ACT.12: 3 residues within 4Å: Chain D: F.263, S.266, S.268 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:S.268, D:F.263 Hydrophobic interactions: D:F.263

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: E.235, K.238, R.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.238, A:K.238, A:R.242, A:R.242 Water bridges: A:E.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borsari, C. et al., Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs. J.Med.Chem. (2016)

Release Date

2016-08-17

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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