SMTL ID : 5izc.1

Trypanosoma brucei PTR1 in complex with inhibitor F032

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 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.10, K.13, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: 6F4.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:P.204 Hydrogen bonds: A:R.14, A:I.15, A:H.35, A:N.36, A:N.36, A:S.37, A:D.62, A:L.63, A:T.64, A:T.64, A:N.93, A:S.95, A:S.95, A:S.95, A:Y.174, A:K.178, A:S.207, A:L.208 Water bridges: A:A.12, A:A.12, A:K.13, A:K.13, A:R.14, A:G.16, A:H.35, A:H.35, A:S.37, A:N.93 Salt bridges: A:K.13, A:R.14, A:R.14 NAP.5: 27 residues within 4Å: Chain B: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: 6F4.6 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.14, B:I.15, B:H.35, B:N.36, B:N.36, B:S.37, B:D.62, B:D.62, B:L.63, B:T.64, B:T.64, B:N.93, B:S.95, B:S.95, B:S.95, B:Y.174, B:K.178, B:S.207, B:L.208 Water bridges: B:G.16, B:H.35, B:H.35, B:N.93, B:S.95 Salt bridges: B:R.14, B:R.14 NAP.8: 27 residues within 4Å: Chain C: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: 6F4.9 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.204 Hydrogen bonds: C:I.15, C:H.35, C:N.36, C:N.36, C:S.37, C:D.62, C:L.63, C:T.64, C:N.93, C:S.95, C:S.95, C:S.95, C:K.178, C:S.207, C:L.208 Water bridges: C:R.14, C:R.14, C:G.16, C:N.93, C:S.95 Salt bridges: C:R.14, C:R.14 NAP.11: 27 residues within 4Å: Chain D: G.10, R.14, I.15, H.33, Y.34, H.35, N.36, S.37, A.61, D.62, L.63, T.64, N.93, A.94, S.95, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: 6F4.12 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: D:R.14, D:I.15, D:H.35, D:N.36, D:N.36, D:S.37, D:D.62, D:D.62, D:L.63, D:T.64, D:N.93, D:S.95, D:S.95, D:S.95, D:K.178, D:S.207, D:L.208 Water bridges: D:A.12, D:A.12, D:G.16, D:T.64, D:N.93, D:S.95 Salt bridges: D:R.14, D:R.14

4 x 6F4: N~2~-[(thiophen-2-yl)methyl]-1,3,4-thiadiazole-2,5-diamine(Non-covalent)

6F4.2: 10 residues within 4Å: Chain A: S.95, F.97, C.168, Y.174, V.206, L.209, P.210, M.213, W.221 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.97, A:P.210 Hydrogen bonds: A:S.95, A:S.95, A:Y.174 Water bridges: A:F.97 pi-Stacking: A:F.97, A:W.221, A:W.221 6F4.6: 8 residues within 4Å: Chain B: S.95, F.97, C.168, Y.174, V.206, P.210, W.221 Ligands: NAP.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.206 Hydrogen bonds: B:S.95, B:S.95, B:Y.174 pi-Stacking: B:F.97, B:W.221, B:W.221 6F4.9: 9 residues within 4Å: Chain C: S.95, F.97, C.168, Y.174, V.206, L.209, P.210, W.221 Ligands: NAP.8 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.206, C:L.209 Hydrogen bonds: C:S.95, C:S.95 Water bridges: C:F.97 pi-Stacking: C:F.97, C:W.221 6F4.12: 9 residues within 4Å: Chain D: S.95, F.97, C.168, Y.174, V.206, P.210, M.213, W.221 Ligands: NAP.11 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.97 Hydrogen bonds: D:S.95, D:S.95 Water bridges: D:F.97 pi-Stacking: D:F.97, D:W.221, D:W.221

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

ACT.3: 3 residues within 4Å: Chain A: K.13, R.14, R.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.13, A:R.14 Hydrogen bonds: A:R.14 Salt bridges: A:R.17 ACT.4: 4 residues within 4Å: Chain A: N.65, V.120 Chain C: N.65, V.120 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.120 Hydrogen bonds: A:N.65, C:N.65 Water bridges: A:A.121 ACT.10: 2 residues within 4Å: Chain C: V.57, V.58 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.58 Hydrogen bonds: C:V.58 Water bridges: C:N.49

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain B: D.46, V.57, V.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.58 Water bridges: B:N.49, B:V.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linciano, P. et al., Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery. ACS Omega (2017)

Release Date

2017-04-05

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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