SMTL ID : 6kk0.1 (1 other biounit)

Crystal structure of PDE4D catalytic domain complexed with compound 4e

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x M36: 7-[8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-5-oxidanyl-6-oxidanylidene-pyrano[3,2-b]xanthen-9-yl]oxyheptanoic acid(Non-covalent)

M36.1: 14 residues within 4Å: Chain A: Y.74, H.75, H.79, D.116, M.188, D.233, L.234, M.272, K.282, S.283, G.286, F.287 Ligands: ZN.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.74, A:L.234, A:F.287 Salt bridges: A:H.75, A:H.79

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.79, H.115, D.116, D.233 Ligands: M36.1, MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.79, A:H.115, A:D.116, A:D.233, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.115, D.116 Ligands: M36.1, ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.116, H2O.3, H2O.3, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liang, J. et al., Discovery and Optimization of alpha-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia. J.Med.Chem. (2020)

Release Date

2020-03-18

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cAMP-specific 3',5'-cyclic phosphodiesterase 4D

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