SMTL ID : 5g2b.1 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-008

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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.2, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x LQY: N-(2-amino-2-oxoethyl)-5'-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2'-methoxy[1,1'-biphenyl]-4-carboxamide(Non-covalent)

LQY.3: 16 residues within 4Å: Chain A: H.111, M.227, D.264, I.265, N.267, V.282, T.283, F.286, Y.287, M.303, N.309, E.311, L.312, G.315, Q.316, F.319 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.265, A:F.286, A:F.286, A:F.319 Hydrogen bonds: A:T.283, A:Y.287, A:M.303, A:Q.316 pi-Stacking: A:F.319

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

FMT.4: 3 residues within 4Å: Chain A: F.87, E.210 Ligands: GAI.8 No protein-ligand interaction detected (PLIP) FMT.5: 4 residues within 4Å: Chain A: E.207, G.208, 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.6: 5 residues within 4Å: Chain A: S.46, F.47, D.48, D.51, R.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.48, A:R.58

2 x GAI: GUANIDINE(Non-covalent)

GAI.7: 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:L.195, A:R.211 Water bridges: A:D.204 Salt bridges: A:D.201, A:D.204 GAI.8: 3 residues within 4Å: Chain A: K.86, E.138 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.138 Salt bridges: A:E.138

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

2017-11-29

Peptides

CLASS 1 PHOSPHODIESTERASE PDEB1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CLASS 1 PHOSPHODIESTERASE PDEB1

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