SMTL ID : 6fdw.2 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x D62: (4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one(Non-covalent)

D62.1: 12 residues within 4Å: Chain A: H.111, M.227, D.264, I.265, N.267, A.279, V.282, F.286, M.303, Q.316, G.318, F.319 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.265, A:F.286, A:F.319 Hydrogen bonds: A:Q.316, A:G.318 pi-Stacking: A:F.319

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.115, H.151, D.152, D.264 Ligands: MG.3 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.3: 2 residues within 4Å: Chain A: D.152 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.152, H2O.1, H2O.1, H2O.2, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., TbrPDEB1 structure with inhibitor NPD-356. To be published

Release Date

2019-04-10

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphodiesterase

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