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

Crystal structure of PDE4D catalytic domain complexed with compound 1

Coordinates

PDB Format Compare

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.80, H.116, D.117, D.234 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.80, A:H.116, A:D.117, A:D.234, H2O.2, H2O.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.116, D.117, E.146 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.117, H2O.1, H2O.1, H2O.2, H2O.2, H2O.3

1 x MKU: 5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one(Non-covalent)

MKU.3: 10 residues within 4Å: Chain A: Y.75, M.189, N.237, P.238, W.248, T.249, I.252, M.273, Q.285, F.288 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:M.189, A:P.238, A:I.252, A:I.252 Hydrogen bonds: A:Q.285 pi-Stacking: A:F.288, A:F.288

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
B

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

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