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

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-226

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.3

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.1 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.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.133, L.136, T.137, E.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.136, A:E.138 Water bridges: A:L.136

2 x GAI: GUANIDINE(Non-covalent)

GAI.4: 4 residues within 4Å: Chain A: D.204, L.206, E.207, R.211 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.204, A:L.206 Water bridges: A:G.208 Salt bridges: A:D.204, A:E.207 GAI.5: 5 residues within 4Å: Chain A: G.130, N.131, C.335, Q.337, G.338 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.130, A:N.131, A:C.335, A:Q.337, A:G.338 Salt bridges: A:E.134

1 x D5T: 1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione(Non-covalent)

D5T.6: 14 residues within 4Å: Chain A: Y.110, H.111, M.227, D.264, I.265, N.267, W.278, A.279, V.282, M.303, Q.316, G.318, F.319, F.322 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.265, A:F.319, A:F.322 Hydrogen bonds: A:Q.316 Water bridges: A:A.279 pi-Stacking: A:F.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., TbrPDEB1 structure with inhibitor NPD-226. 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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