SMTL ID : 2qhx.1

Structure of Pteridine Reductase from Leishmania major complexed with a ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-tetramer

Ligands

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 5 residues within 4Å: Chain A: N.108, T.180, F.184 Chain B: N.108 Ligands: IOD.4 Ligand excluded by PLIP IOD.4: 6 residues within 4Å: Chain A: N.108 Chain B: N.108, T.180, A.181, F.184 Ligands: IOD.1 Ligand excluded by PLIP

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 28 residues within 4Å: Chain A: G.53, R.57, L.58, H.76, Y.77, H.78, R.79, S.80, A.104, D.105, L.106, S.107, N.149, A.150, S.151, S.152, D.182, S.186, M.219, V.220, D.221, Y.234, K.238, P.264, G.265, L.266, S.267 Ligands: FE1.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:P.264 Hydrogen bonds: A:R.57, A:L.58, A:H.78, A:R.79, A:S.80, A:L.106, A:S.107, A:N.149, A:S.151, A:S.151, A:S.151, A:D.182, A:Y.234, A:K.238, A:S.267, A:S.267 Water bridges: A:G.53, A:A.55, A:A.55, A:K.56, A:K.56, A:G.59, A:H.78, A:H.78, A:N.149 Salt bridges: A:R.57, A:R.57 pi-Stacking: A:H.78 NAP.5: 28 residues within 4Å: Chain B: G.53, R.57, L.58, H.76, Y.77, H.78, R.79, S.80, A.104, D.105, L.106, S.107, N.149, A.150, S.151, S.152, D.182, S.186, M.219, V.220, D.221, Y.234, K.238, P.264, G.265, L.266, S.267 Ligands: FE1.6 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.264 Hydrogen bonds: B:R.57, B:L.58, B:H.78, B:R.79, B:S.80, B:D.105, B:L.106, B:S.107, B:N.149, B:S.151, B:S.151, B:S.151, B:D.182, B:D.182, B:K.238, B:S.267, B:S.267 Water bridges: B:A.55, B:K.56, B:G.59, B:S.80, B:N.149 Salt bridges: B:R.57, B:R.57 pi-Stacking: B:H.78 NAP.7: 27 residues within 4Å: Chain C: G.53, R.57, L.58, H.76, Y.77, H.78, R.79, S.80, A.104, D.105, L.106, S.107, N.149, A.150, S.151, S.152, D.182, M.219, V.220, D.221, Y.234, K.238, P.264, G.265, L.266, S.267 Ligands: FE1.8 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:P.264 Hydrogen bonds: C:R.57, C:L.58, C:H.78, C:R.79, C:S.80, C:L.106, C:S.107, C:N.149, C:S.151, C:S.151, C:S.151, C:D.182, C:Y.234, C:K.238, C:S.267, C:S.267 Water bridges: C:G.53, C:A.55, C:A.55, C:K.56, C:R.57, C:G.59, C:H.78, C:H.78, C:S.80, C:N.149 Salt bridges: C:R.57, C:R.57 pi-Stacking: C:H.78 NAP.9: 28 residues within 4Å: Chain D: G.53, R.57, L.58, H.76, Y.77, H.78, R.79, S.80, A.104, D.105, L.106, S.107, N.149, A.150, S.151, S.152, D.182, S.186, M.219, V.220, D.221, Y.234, K.238, P.264, G.265, L.266, S.267 Ligands: FE1.10 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:P.264 Hydrogen bonds: D:R.57, D:L.58, D:H.78, D:R.79, D:S.80, D:D.105, D:L.106, D:S.107, D:N.149, D:S.151, D:S.151, D:S.151, D:D.182, D:K.238, D:S.267, D:S.267 Water bridges: D:G.53, D:A.55, D:A.55, D:S.80, D:S.80, D:N.149, D:N.149 Salt bridges: D:R.57, D:R.57 pi-Stacking: D:H.78

4 x FE1: METHYL 1-(4-{[(2,4-DIAMINOPTERIDIN-6-YL)METHYL](METHYL)AMINO}BENZOYL)PIPERIDINE-4-CARBOXYLATE(Non-covalent)

FE1.3: 13 residues within 4Å: Chain A: R.57, S.151, F.153, D.221, L.228, Y.231, Y.234, G.265, L.266, L.269, D.272, H.281 Ligands: NAP.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.228 Hydrogen bonds: A:R.57, A:S.151, A:D.221, A:Y.234 pi-Stacking: A:F.153 FE1.6: 11 residues within 4Å: Chain B: R.57, S.151, F.153, D.221, L.228, Y.231, Y.234, L.266, L.269, M.273 Ligands: NAP.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.153, B:L.228, B:Y.231 Hydrogen bonds: B:R.57, B:S.151, B:S.151, B:D.221 pi-Stacking: B:F.153 FE1.8: 10 residues within 4Å: Chain C: R.57, S.151, F.153, D.221, L.228, Y.231, Y.234, L.266, L.269 Ligands: NAP.7 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.228 Hydrogen bonds: C:R.57, C:S.151, C:S.152, C:Y.234, C:Y.234 Water bridges: C:R.57 pi-Stacking: C:F.153, C:F.153, C:F.153 FE1.10: 12 residues within 4Å: Chain D: R.57, S.151, F.153, Y.154, P.155, D.221, L.228, Y.231, Y.234, L.266, L.269 Ligands: NAP.9 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.228 Hydrogen bonds: D:R.57, D:S.151, D:S.152, D:Y.234 Water bridges: D:R.57 pi-Stacking: D:F.153, D:F.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazzuti, A. et al., Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2007-12-25

Peptides

Pteridine reductase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pteridine reductase 1