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

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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.1, H2O.3

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.1, H2O.2, H2O.2, H2O.3, H2O.3

3 x GAI: GUANIDINE(Non-covalent)

GAI.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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.336, A:Q.337, A:G.338 Salt bridges: A:E.134 GAI.4: 2 residues within 4Å: Chain A: T.137, E.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.138 Water bridges: A:L.139 Salt bridges: A:E.138 GAI.5: 6 residues within 4Å: Chain A: L.195, S.196, D.197, P.198, D.201, D.204 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.195, A:R.211 Salt bridges: A:D.201, A:D.204

1 x E3Q: 1-cycloheptyl-3-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-4,4-dimethyl-4,5-dihydro- 1H-pyrazol-5-one(Non-covalent)

E3Q.6: 12 residues within 4Å: Chain A: M.227, I.265, N.267, A.279, V.282, T.283, F.286, M.303, L.312, G.315, Q.316, F.319 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

Singh, A.K. et al., Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-637. To be published

Release Date

2019-03-13

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphodiesterase

Related Entries With Identical Sequence