SMTL ID : 8of2.1

Trypanosoma brucei pteridine reductase 1 (TbPTR1) in complex with 2,4,6 triamminopyrimidine (TAP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-tetramer

Ligands

4 x 3AY: PYRIMIDINE-2,4,6-TRIAMINE(Non-covalent)

3AY.1: 8 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, L.228, P.230 Ligands: NDP.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.117 Hydrogen bonds: A:R.34, A:S.115, A:S.115, A:Y.194, A:L.228 pi-Stacking: A:F.117 pi-Cation interactions: A:F.117 3AY.4: 6 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194 Ligands: NDP.3 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.34, B:S.115, B:S.115, B:Y.194, B:Y.194, B:L.228 pi-Stacking: B:F.117 3AY.7: 8 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.228, P.230 Ligands: NDP.6 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.34, C:S.115, C:S.115, C:Y.194, C:L.228 pi-Stacking: C:F.117 3AY.10: 6 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194 Ligands: NDP.9 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.34, D:S.115, D:S.115, D:Y.194, D:Y.194 Water bridges: D:L.228 pi-Stacking: D:F.117

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 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: 3AY.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:P.224 Hydrogen bonds: A:R.34, A:I.35, A:H.55, A:N.56, A:N.56, A:S.57, A:D.82, A:D.82, A:L.83, A:T.84, A:N.113, A:S.115, A:S.115, A:S.115, A:K.198, A:S.227, A:L.228 Water bridges: A:G.36, A:N.113 Salt bridges: A:R.34, A:R.34 NDP.3: 28 residues within 4Å: Chain B: 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: 3AY.4 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:N.56, B:N.56, B:S.57, 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:R.34, B:G.36, B:H.55, B:H.55, B:S.57, B:S.57, B:N.113 Salt bridges: B:R.34, B:R.34 NDP.6: 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: 3AY.7 25 PLIP interactions: 25 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:G.30, C:G.36, C:S.57, C:S.57, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NDP.9: 26 residues within 4Å: Chain D: 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: 3AY.10 27 PLIP interactions: 27 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:T.84, D:N.113, D:S.115, D:S.115, D:S.115, D:Y.194, D:K.198, D:S.227, D:L.228 Water bridges: D:A.32, D:A.32, D:G.36, D:N.113 Salt bridges: D:R.34, D:R.34

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain B: N.85, V.140, A.141 Chain C: N.85 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:A.141 Hydrogen bonds: C:N.85

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

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.11: 4 residues within 4Å: Chain D: A.232, M.233, G.234, E.235 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.235 Water bridges: D:K.238, D:K.238 Salt bridges: D:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linciano, P. et al., The discovery of aryl-2-nitroethyl triamino pyrimidines as anti-Trypanosoma brucei agents. Eur.J.Med.Chem. (2023)

Release Date

2023-12-13

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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