SMTL ID : 5l8c.1 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-039

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.115, H.151, D.152, D.264 Ligands: MG.2 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.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.152, T.225 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.1, H2O.3, H2O.4, H2O.4

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

FMT.3: 3 residues within 4Å: Chain A: K.86, F.87, E.210 No protein-ligand interaction detected (PLIP) FMT.4: 3 residues within 4Å: Chain A: E.207, A.209, E.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.209, A:E.210 Water bridges: A:E.207 FMT.5: 4 residues within 4Å: Chain A: S.46, F.47, D.48, F.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.48

1 x GAI: GUANIDINE(Non-covalent)

GAI.6: 2 residues within 4Å: Chain A: L.357, R.360 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.357, A:L.357 Water bridges: A:R.360, A:R.360, A:R.360

1 x 908: 4-[5-[(4~{a}~{R},8~{a}~{S})-4-oxidanylidene-3-propan-2-yl-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(2-azanyl-2-oxidanylidene-ethyl)benzamide(Non-covalent)

908.7: 16 residues within 4Å: Chain A: M.227, D.264, I.265, N.267, A.279, V.282, T.283, F.286, Y.287, M.303, N.309, E.311, L.312, G.315, Q.316, F.319 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:M.227, A:I.265, A:V.282, A:F.286, A:F.319 Hydrogen bonds: A:E.311, A:Q.316 pi-Stacking: A:F.319

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: G.130, N.131, V.132, E.134, K.135, C.335, L.336, Q.337, G.338 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.130, A:E.134, A:Q.337, A:G.338 Water bridges: A:K.135, A:C.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaazer, A.R. et al., Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. (2018)

Release Date

2018-03-14

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphodiesterase

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