SMTL ID : 5g5v.1 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 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.3, H2O.4

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

6 x GAI: GUANIDINE(Non-covalent)

GAI.3: 7 residues within 4Å: Chain A: D.154, H.155, M.156, Y.163, L.170, L.183, H.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.154, A:M.156 GAI.4: 6 residues within 4Å: Chain A: S.46, F.47, D.48, D.51, F.54 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.46, A:D.48, A:D.48 Salt bridges: A:D.51 GAI.5: 8 residues within 4Å: Chain A: H.111, H.155, G.157, L.158, N.159, E.285, F.286, Q.289 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.111, A:Q.289 Salt bridges: A:E.285 GAI.14: 2 residues within 4Å: Chain A: G.88, S.90 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.88 Water bridges: A:G.88, A:S.90 GAI.17: 5 residues within 4Å: Chain A: E.134, K.135, L.136, T.137, H.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.134, A:L.136, A:H.252 GAI.18: 4 residues within 4Å: Chain A: K.86, F.87, G.88, G.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.87

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 2 residues within 4Å: Chain A: R.129, W.341 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.129 EDO.7: 6 residues within 4Å: Chain A: R.36, L.40, Y.75, D.91, E.92 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: G.80, S.81, H.124, Y.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.124 EDO.9: 7 residues within 4Å: Chain A: F.57, R.60, P.109, N.112, Y.114, W.278, A.281 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:N.112, A:N.112 Water bridges: A:Q.277 EDO.10: 7 residues within 4Å: Chain A: S.161, K.165, Q.289, E.293, V.300, L.301, F.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.289, A:L.301 Water bridges: A:N.159, A:N.159, A:K.165 EDO.11: 3 residues within 4Å: Chain A: K.33, R.36 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.36 EDO.12: 6 residues within 4Å: Chain A: F.47, E.53, F.54, D.55, R.58 Ligands: GAI.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.55 Water bridges: A:E.53 EDO.15: 2 residues within 4Å: Chain A: Q.85, D.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.85 Water bridges: A:D.91 EDO.16: 9 residues within 4Å: Chain A: G.130, N.131, V.132, E.134, K.135, C.335, L.336, Q.337, G.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.336, A:Q.337, A:G.338 EDO.20: 3 residues within 4Å: Chain A: R.211, T.212, F.215 No protein-ligand interaction detected (PLIP)

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

FMT.13: 6 residues within 4Å: Chain A: L.195, S.196, D.197, P.198, D.201, D.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.201, A:D.204 Water bridges: A:R.211

1 x 8Z4: (4AS,8AR)-4-(3-{4-[(3R)-3-HYDROXYPYRROLIDINE-1-(Non-covalent)

8Z4.19: 13 residues within 4Å: Chain A: M.227, D.264, I.265, V.282, T.283, F.286, Y.287, M.303, N.309, L.312, G.315, Q.316, F.319 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.265, A:T.283, A:F.286, A:Y.287, A:F.319 Hydrogen bonds: A:T.283, A:N.309, A:Q.316 Water bridges: A:G.315 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 B1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHODIESTERASE B1

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