SMTL ID : 2yhu.1

Trypanosoma brucei PTR1 in complex with inhibitor WHF30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

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

NDP.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: WHF.2 28 PLIP interactions: 28 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: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:G.36, A:H.55, A:H.55, A:S.57, A:N.113 Salt bridges: A:R.34, A:R.34 pi-Stacking: A:H.55 NDP.3: 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: WHF.4 26 PLIP interactions: 26 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.36, B:H.55, B:N.113 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NDP.6: 26 residues within 4Å: Chain C: 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: WHF.7 21 PLIP interactions: 21 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:L.83, C:T.84, 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 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NDP.8: 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: WHF.9 23 PLIP interactions: 23 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:N.113 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x WHF: 3-(5-AMINO-1,3,4-THIADIAZOL-2-YL)-1-THIOPHEN-2-YLPROPAN-1-ONE(Non-covalent)

WHF.2: 8 residues within 4Å: Chain A: S.115, F.117, C.188, Y.194, L.229, P.230, W.241 Ligands: NDP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.117, A:F.117 Hydrogen bonds: A:S.115, A:Y.194 pi-Stacking: A:F.117, A:W.241, A:W.241 WHF.4: 9 residues within 4Å: Chain B: S.115, F.117, C.188, Y.194, V.226, L.229, P.230, W.241 Ligands: NDP.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.117, B:V.226 Hydrogen bonds: B:S.115, B:Y.194 pi-Stacking: B:F.117, B:W.241, B:W.241 WHF.7: 11 residues within 4Å: Chain C: S.115, F.117, C.188, Y.194, G.225, V.226, L.229, P.230, M.233, W.241 Ligands: NDP.6 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.117 Hydrogen bonds: C:S.115 pi-Stacking: C:F.117, C:W.241, C:W.241 WHF.9: 10 residues within 4Å: Chain D: S.115, F.117, C.188, Y.194, G.225, V.226, P.230, M.233, W.241 Ligands: NDP.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.226, D:P.230 Hydrogen bonds: D:S.115 Water bridges: D:Y.194, D:Y.194 pi-Stacking: D:F.117, D:W.241, D:W.241

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

ACT.5: 2 residues within 4Å: Chain B: Y.54, V.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.54 ACT.10: 5 residues within 4Å: Chain B: M.156 Chain D: T.120, P.121, Q.124, Q.139 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Q.124 Hydrogen bonds: D:P.121, D:Q.124, D:Q.139

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

2012-05-23

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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