SMTL ID : 2yhi.1

Trypanosoma brucei PTR1 in complex with inhibitor WH16

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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: W16.2 27 PLIP interactions: 27 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:G.36, A:N.113, A:S.115 Salt bridges: A:K.33, A:R.34, A:R.34 pi-Stacking: A:H.55 NAP.5: 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: W16.6 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:L.83, B:T.84, B:N.113, B:S.115, B:S.115, B:S.115, B:K.198, B:S.227, B:L.228 Water bridges: B:K.33, B:R.34, B:G.36, B:S.57, B:N.113, B:S.115 Salt bridges: B:R.34, B:R.34 pi-Stacking: B:H.55 NAP.8: 28 residues within 4Å: Chain C: 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: W16.9 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:P.224 Hydrogen bonds: C:K.33, C:R.34, C:I.35, C:H.55, C:N.56, C:N.56, C:S.57, C:D.82, 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:R.34, C:G.36, C:S.57, C:S.57, C:N.113, C:S.115 Salt bridges: C:R.34, C:R.34 pi-Stacking: C:H.55 NAP.11: 28 residues within 4Å: Chain D: 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: W16.12 30 PLIP interactions: 30 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: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:R.34, D:G.36, D:H.55, D:H.55, D:S.57, D:S.57, D:N.113 Salt bridges: D:R.34, D:R.34 pi-Stacking: D:H.55

4 x W16: 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE(Non-covalent)

W16.2: 9 residues within 4Å: Chain A: F.117, D.181, Y.194, V.226, P.230, M.233, W.241 Ligands: NAP.1, DTV.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.194, A:Y.194 pi-Stacking: A:F.117 W16.6: 9 residues within 4Å: Chain B: F.117, D.181, Y.194, V.226, P.230, M.233, W.241 Ligands: NAP.5, DTU.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.194, B:Y.194 pi-Stacking: B:F.117 W16.9: 7 residues within 4Å: Chain C: F.117, D.181, Y.194, P.230, W.241 Ligands: NAP.8, DTT.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.194 pi-Stacking: C:F.117 W16.12: 9 residues within 4Å: Chain D: F.117, D.181, Y.194, V.226, P.230, M.233, W.241 Ligands: NAP.11, DTT.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.194, D:Y.194 pi-Stacking: D:F.117

1 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.3: 8 residues within 4Å: Chain A: F.117, C.188, F.191, M.233, E.237, W.241 Ligands: W16.2, ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.237 Water bridges: A:M.189

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

ACT.4: 5 residues within 4Å: Chain A: F.117, Y.118, P.119, A.232 Ligands: DTV.3 No protein-ligand interaction detected (PLIP) ACT.14: 4 residues within 4Å: Chain D: F.117, Y.118, P.119 Ligands: DTT.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.117

1 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Covalent)

DTU.7: 8 residues within 4Å: Chain B: F.117, C.188, F.191, M.233, E.237, W.241 Chain D: H.287 Ligands: W16.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.241

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.10: 6 residues within 4Å: Chain A: H.287 Chain C: C.188, F.191, M.233, W.241 Ligands: W16.9 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:M.189, A:H.287 DTT.13: 8 residues within 4Å: Chain D: F.117, C.188, F.191, M.233, E.237, W.241 Ligands: W16.12, ACT.14 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.287

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, PUTATIVE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PTERIDINE REDUCTASE, PUTATIVE

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