SMTL ID : 6fe3.1 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1439

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

5 x GAI: GUANIDINE(Non-covalent)

GAI.1: 6 residues within 4Å: Chain A: L.195, S.196, P.198, D.201, D.204, R.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.196, A:R.211 Water bridges: A:D.204 Salt bridges: A:D.201, A:D.204 GAI.2: 1 residues within 4Å: Chain A: R.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.355, A:R.355 GAI.10: 3 residues within 4Å: Chain A: R.253, M.254, E.257 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.220, A:A.249, A:R.253 Salt bridges: A:E.257 GAI.11: 3 residues within 4Å: Chain A: K.86, F.87, E.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.86 Salt bridges: A:E.210 GAI.12: 1 residues within 4Å: Chain A: E.134 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.134

1 x D68: 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione(Non-covalent)

D68.3: 17 residues within 4Å: Chain A: H.111, M.227, D.264, I.265, N.267, V.268, W.278, A.279, V.282, F.286, M.303, G.315, Q.316, G.318, F.319, F.322, V.323 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.265, A:V.282, A:F.322 Hydrogen bonds: A:Q.316 Water bridges: A:A.279, A:F.319 pi-Stacking: A:F.319 Halogen bonds: A:G.315

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.115, H.151, D.152, D.264 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.115, A:H.151, A:D.152, A:D.264, H2O.1, H2O.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: D.152 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.3, H2O.4, H2O.5, H2O.7

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 6 residues within 4Å: Chain A: G.88, C.89, S.90, V.93, D.204 Ligands: FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.90, A:S.90 Water bridges: A:D.204 FMT.7: 4 residues within 4Å: Chain A: G.88, D.204, G.205 Ligands: FMT.6 No protein-ligand interaction detected (PLIP) FMT.8: 2 residues within 4Å: Chain A: N.131, G.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.131, A:Q.337, A:G.338 FMT.9: 2 residues within 4Å: Chain A: A.239, A.242 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., TbrPDEB1 structure with inhibitor NPD-1439. To be published

Release Date

2019-04-10

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphodiesterase

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