SMTL ID : 5jdc.1

Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 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.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: 6JP.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, 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.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: 6JP.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:G.30, B:A.32, B:G.36, B:N.113 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.6: 26 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 Ligands: 6JP.7 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.30, 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:S.227 Water bridges: C:A.32, C:G.36, C:N.113 Salt bridges: C:R.34, C:R.34 NAP.10: 26 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, Y.194, K.198, P.224, G.225, V.226, S.227, L.228 Ligands: 6JP.11 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: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:A.32, D:G.36, D:N.113 Salt bridges: D:R.34, D:R.34

4 x 6JP: (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one(Non-covalent)

6JP.2: 14 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, L.228, L.229, P.230, W.241 Chain D: H.287 Ligands: NAP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.241 Hydrogen bonds: A:R.34, A:S.115, A:D.181, A:L.228 pi-Stacking: A:F.117 6JP.5: 14 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, M.183, Q.186, P.187, C.188, Y.194, L.228, L.229, P.230, W.241 Ligands: NAP.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.241 Hydrogen bonds: B:R.34, B:S.115, B:D.181, B:L.228 pi-Stacking: B:F.117 6JP.7: 13 residues within 4Å: Chain B: H.287 Chain C: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, L.229, P.230, W.241 Ligands: NAP.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.241 Hydrogen bonds: C:R.34, C:S.115, C:D.181 pi-Stacking: C:F.117 6JP.11: 15 residues within 4Å: Chain A: H.287 Chain D: R.34, S.115, F.117, D.181, M.183, Q.186, C.188, Y.194, V.226, L.228, L.229, P.230, W.241 Ligands: NAP.10 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.226, D:W.241 Hydrogen bonds: D:R.34, D:S.115, D:D.181, D:Y.194 pi-Stacking: 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.8: 3 residues within 4Å: Chain C: A.65, V.77, V.78 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.65 Hydrogen bonds: C:V.78

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 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

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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