SMTL ID : 5g57.2 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x 6M5: (4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one(Non-covalent)

6M5.1: 14 residues within 4Å: Chain A: M.227, D.264, I.265, N.267, A.279, V.282, F.286, L.301, M.303, F.304, G.315, Q.316, F.319, V.323 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.265, A:F.286, A:F.304, A:V.323 Hydrogen bonds: A:Q.316 Water bridges: A:N.159 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.3, H2O.4

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.3, H2O.4, H2O.4, H2O.4, H2O.5

4 x GAI: GUANIDINE(Non-covalent)

GAI.4: 2 residues within 4Å: Chain A: V.52, R.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.129 Water bridges: A:D.51, A:R.129 pi-Cation interactions: A:W.341 GAI.9: 6 residues within 4Å: Chain A: R.106, D.154, M.156, Y.163, L.170, H.186 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.106, A:Y.163, A:Y.163, A:Y.163, A:H.186 Salt bridges: A:D.154 GAI.10: 4 residues within 4Å: Chain A: D.204, L.206, E.207, R.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.206 Salt bridges: A:D.204, A:E.207 GAI.11: 2 residues within 4Å: Chain A: T.50, G.80 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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:T.137 Water bridges: A:E.138, A:E.138 GOL.6: 8 residues within 4Å: Chain A: G.130, N.131, V.132, E.134, K.135, L.336, Q.337, G.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.135, A:G.338, A:M.339 GOL.7: 4 residues within 4Å: Chain A: L.67, R.102, Y.105, F.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.102 Water bridges: A:R.106, A:R.106, A:F.113 GOL.8: 2 residues within 4Å: Chain A: K.86, E.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.86, A:K.86 Water 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

PHOSPHODIESTERASE B1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

PHOSPHODIESTERASE B1

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