SMTL ID : 6ftm.1 (1 other biounit)

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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.3, H2O.3, H2O.5

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.5

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

EDO.3: 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.4: 4 residues within 4Å: Chain A: A.351, E.354, R.355, E.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.355, A:R.355 EDO.5: 7 residues within 4Å: Chain A: S.161, K.165, Q.289, E.293, V.300, L.301, F.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.165, A:Q.289, A:L.301 EDO.6: 7 residues within 4Å: Chain A: F.57, R.60, P.109, N.112, Y.114, W.278, A.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.60, A:R.60, A:N.112, A:N.112 EDO.7: 4 residues within 4Å: Chain A: K.65, P.66, L.67, D.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.67 EDO.8: 6 residues within 4Å: Chain A: K.33, R.36, E.37, L.40, E.92 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.92, A:E.92 EDO.9: 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.10: 2 residues within 4Å: Chain A: R.106, N.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.106, A:N.107 EDO.11: 3 residues within 4Å: Chain A: N.107, V.108, P.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.107 EDO.12: 4 residues within 4Å: Chain A: R.216, S.217, D.220, R.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.217 Water bridges: A:D.220 EDO.13: 4 residues within 4Å: Chain A: Y.75, D.91, E.92 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.92 EDO.14: 3 residues within 4Å: Chain A: V.52, R.129, W.341 No protein-ligand interaction detected (PLIP)

8 x GAI: GUANIDINE(Non-covalent)

GAI.15: 7 residues within 4Å: Chain A: D.154, H.155, M.156, Y.163, L.170, L.183, H.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.154, A:D.154, A:M.156 GAI.16: 6 residues within 4Å: Chain A: S.46, F.47, D.48, D.51, E.53, F.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.46, A:D.48, A:D.48 Water bridges: A:D.55 Salt bridges: A:D.51 GAI.17: 4 residues within 4Å: Chain A: G.80, S.81, H.124, Y.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.80 pi-Cation interactions: A:Y.128 GAI.18: 4 residues within 4Å: Chain A: K.86, F.87, G.88, G.205 No protein-ligand interaction detected (PLIP) GAI.19: 2 residues within 4Å: Chain A: T.137, E.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.138 Water bridges: A:T.137, A:L.139 Salt bridges: A:E.138 GAI.20: 5 residues within 4Å: Chain A: S.232, A.233, M.254, E.257 Ligands: GAI.21 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.232, A:A.236 Salt bridges: A:E.257 GAI.21: 5 residues within 4Å: Chain A: D.220, A.224, K.229, E.257 Ligands: GAI.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.220 Salt bridges: A:D.220, A:E.257 GAI.22: 6 residues within 4Å: Chain A: Y.287, M.303, N.309, K.314, G.315 Ligands: E6Z.26 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.287, A:Y.287, A:M.303, A:K.314, A:K.314

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

FMT.23: 6 residues within 4Å: Chain A: L.195, S.196, P.198, D.201, D.204, R.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.196, A:D.201, A:R.211 FMT.24: 5 residues within 4Å: Chain A: S.81, L.83, K.86, Y.128, E.138 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.138 Water bridges: A:Y.128 FMT.25: 5 residues within 4Å: Chain A: E.134, K.135, L.136, T.137, H.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.134 Water bridges: A:E.248 FMT.27: 2 residues within 4Å: Chain A: R.211, T.212 No protein-ligand interaction detected (PLIP)

1 x E6Z: 3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide(Non-covalent)

E6Z.26: 11 residues within 4Å: Chain A: M.227, D.264, I.265, N.267, V.282, F.286, M.303, G.315, Q.316, F.319 Ligands: GAI.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.265, A:F.286 Hydrogen bonds: A:Q.316 pi-Stacking: A:F.319

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Heuvel, E. et al., Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048. To be published

Release Date

2019-03-20

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphodiesterase

Related Entries With Identical Sequence