SMTL ID : 2wd8.1

PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00071204

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

3 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, A.96, T.126, L.159, C.160, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGF.3 27 PLIP interactions: 27 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: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:H.35, A:S.37, A:S.37, A:S.95, A:A.96 Salt bridges: A:K.13, A:R.14, A:R.14 pi-Stacking: A:H.35 NAP.4: 26 residues within 4Å: Chain B: 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, A.96, T.126, L.159, C.160, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGF.5 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:P.204 Hydrogen bonds: B:R.14, B:I.15, B:H.35, B:H.35, B:N.36, B:N.36, B:S.37, B:D.62, B:L.63, B:T.64, 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.10, B:A.12, B:A.12, B:G.16, B:N.93, B:A.96 Salt bridges: B:R.14, B:R.14 pi-Stacking: B:H.35 NAP.8: 28 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, A.96, T.126, L.159, C.160, D.161, Y.174, K.178, P.204, G.205, V.206, S.207, L.208 Ligands: VGF.9 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:P.204 Hydrogen bonds: 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:N.93, D:S.95, D:S.95, D:S.95, D:K.178, D:G.205, D:S.207 Water bridges: D:A.12, D:R.14, D:G.16, D:H.35, D:S.37, D:S.37, D:N.93 Salt bridges: D:R.14, D:R.14 pi-Stacking: D:H.35

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: K.13, R.14 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain C: H.33, H.35 Ligand excluded by PLIP

4 x VGF: 1-(3,4-DICHLOROBENZYL)-7-PHENYL-1H-BENZIMIDAZOL-2-AMINE

VGF.3: 16 residues within 4Å: Chain A: F.97, D.161, M.163, C.168, F.171, Y.174, G.205, V.206, L.209, M.213, W.221, K.224, L.263 Chain D: H.267, A.268 Ligands: NAP.1 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.97, A:Y.174, A:V.206, A:L.209, A:L.263 Hydrogen bonds: A:G.205 Water bridges: A:D.161, A:C.168 Salt bridges: A:D.161 pi-Stacking: A:F.97, A:F.171, A:W.221, A:W.221, D:H.267 Halogen bonds: A:W.221, D:A.268 VGF.5: 16 residues within 4Å: Chain B: F.97, D.161, M.163, C.168, F.171, Y.174, P.204, G.205, V.206, L.209, W.221, K.224, L.263 Chain C: H.267, A.268 Ligands: NAP.4 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.97, B:Y.174, B:V.206, B:L.209, B:L.263 Hydrogen bonds: B:G.205 Salt bridges: B:D.161 pi-Stacking: B:F.171, B:W.221, B:W.221 Halogen bonds: B:W.221, C:A.268 VGF.7: 14 residues within 4Å: Chain B: H.267, A.268 Chain C: F.97, D.161, M.163, C.168, F.171, Y.174, G.205, V.206, L.209, W.221, K.224, L.263 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.97, C:Y.174, C:V.206, C:L.209, C:L.263 Hydrogen bonds: C:G.205 Water bridges: C:Y.174 Salt bridges: C:D.161 pi-Stacking: C:F.97, C:F.171, C:W.221, C:W.221, B:H.267 Halogen bonds: C:W.221, B:A.268 VGF.9: 15 residues within 4Å: Chain A: H.267, A.268 Chain D: F.97, D.161, M.163, C.168, F.171, Y.174, P.204, G.205, V.206, W.221, K.224, L.263 Ligands: NAP.8 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.97, D:F.97, D:Y.174, D:V.206, D:L.263 Hydrogen bonds: D:G.205 Salt bridges: D:D.161 pi-Stacking: D:F.171, D:W.221, D:W.221 Halogen bonds: D:W.221, A:A.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mpamhanga, C.P. et al., One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening. J.Med.Chem. (2009)

Release Date

2009-06-30

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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