SMTL ID : 7opj.1

Trypanosoma brucei PTR1 (TbPTR1) in complex with pyrimethamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 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: CP6.2 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:K.33, A:K.33, A:G.36, A:S.57, A:N.113, A:S.115 Salt bridges: A:K.33, A:R.34, A:R.34 NAP.6: 27 residues within 4Å: Chain B: 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: CP6.7, ACT.8 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:A.32, B:G.36, B:H.55, B:H.55, B:S.57, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 NAP.9: 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: CP6.10 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: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.36, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 NAP.12: 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: CP6.13 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: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.36, D:S.57, D:N.113, D:S.115 Salt bridges: D:R.34, D:R.34

4 x CP6: 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE(Non-covalent)

CP6.2: 12 residues within 4Å: Chain A: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.117 Hydrogen bonds: A:S.115, A:S.115, A:D.181, A:Y.194, A:Y.194 pi-Stacking: A:F.117, A:F.117 CP6.7: 11 residues within 4Å: Chain B: R.34, S.115, F.117, D.181, Y.194, V.226, L.229, P.230, W.241 Ligands: NAP.6, ACT.8 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.117, B:P.230 Hydrogen bonds: B:S.115, B:Y.194, B:Y.194 pi-Stacking: B:F.117, B:F.117 CP6.10: 9 residues within 4Å: Chain C: R.34, S.115, F.117, D.181, Y.194, L.228, P.230, W.241 Ligands: NAP.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.117, C:P.230 Hydrogen bonds: C:S.115, C:S.115, C:Y.194 pi-Stacking: C:F.117 CP6.13: 12 residues within 4Å: Chain D: R.34, S.115, F.117, D.181, Y.194, V.226, L.228, L.229, P.230, M.233, W.241 Ligands: NAP.12 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.117, D:P.230 Hydrogen bonds: D:S.115, D:S.115, D:Y.194 pi-Stacking: D:F.117, D:F.117

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

ACT.3: 3 residues within 4Å: Chain A: P.24, T.46, G.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.24 Water bridges: A:Y.48 ACT.4: 3 residues within 4Å: Chain A: K.33, R.34, R.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34 Salt bridges: A:R.37 ACT.5: 3 residues within 4Å: Chain A: F.263, S.266, S.268 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.263 Water bridges: B:S.268 ACT.8: 5 residues within 4Å: Chain B: R.34, P.230, V.231 Ligands: NAP.6, CP6.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.231 Water bridges: B:A.232 Salt bridges: B:R.34

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain C: A.65, V.77, V.78 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.78, C:V.78 Water bridges: C:N.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tassone, G. et al., Evidence of Pyrimethamine and Cycloguanil Analogues as Dual Inhibitors of Trypanosoma brucei Pteridine Reductase and Dihydrofolate Reductase. Pharmaceuticals (2021)

Release Date

2021-07-14

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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