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

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-0769

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 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.5

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

1 x GAI: GUANIDINE(Non-covalent)

GAI.3: 2 residues within 4Å: Chain A: V.52, W.341 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.51, A:R.129

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 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:L.136, A:E.138 GOL.5: 3 residues within 4Å: Chain A: K.86, E.138 Ligands: PEG.8 No protein-ligand interaction detected (PLIP) GOL.6: 8 residues within 4Å: Chain A: G.130, N.131, V.132, E.134, K.135, L.336, Q.337, G.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.130, A:N.131, A:K.135, A:G.338 GOL.7: 5 residues within 4Å: Chain A: L.67, R.102, K.103, Y.105, F.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.113

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 8 residues within 4Å: Chain A: F.87, T.137, E.138, L.139, E.140, E.210, L.213 Ligands: GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.137, A:E.138, A:L.139, A:E.210 Water bridges: A:E.140, A:E.140

1 x J2E: 1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one(Non-covalent)

J2E.9: 10 residues within 4Å: Chain A: H.111, M.227, I.265, N.267, A.279, V.282, F.286, M.303, G.315, Q.316 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.265 Hydrogen bonds: A:Q.316 Water bridges: A:A.279 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-0769. To be published

Release Date

2020-02-05

Peptides

Phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphodiesterase

Related Entries With Identical Sequence