SMTL ID : 5l9h.2 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-340

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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.2

1 x MG: MAGNESIUM ION(Non-covalent)

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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: E.134 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.134, A:K.135 GOL.4: 6 residues within 4Å: Chain A: N.131, K.135, C.335, Q.337, G.338 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.131, A:K.135, A:C.335, A:G.338

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

FMT.5: 5 residues within 4Å: Chain A: L.195, S.196, P.198, D.201, D.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.204

1 x CVL: 5-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4,4-dimethyl-2-propan-2-yl-pyrazol-3-one(Non-covalent)

CVL.6: 9 residues within 4Å: Chain A: M.227, N.267, A.279, V.282, F.286, L.301, M.303, Q.316, F.319 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.286, A:F.319 Hydrogen bonds: A:Q.316 Water bridges: A:M.227, A:A.279 pi-Stacking: A:F.319

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
B

Phosphodiesterase

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