SMTL ID : 7f2l.2 (1 other biounit)

Crystal structure of PDE4D catalytic domain complexed with compound 18a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.164, H.200, D.201, D.318 Ligands: MG.2, 1AS.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.164, A:H.200, A:D.201, A:D.318, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.201 Ligands: ZN.1, 1AS.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.201, H2O.1, H2O.2, H2O.2, H2O.3

1 x 1AS: (~{E})-4-[9-[(4-fluorophenyl)methoxy]-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-6-oxidanylidene-pyrano[3,2-b]xanthen-5-yl]oxybut-2-enoic acid(Non-covalent)

1AS.3: 21 residues within 4Å: Chain A: Y.159, H.160, H.164, D.201, M.273, D.318, L.319, N.321, P.322, W.332, T.333, I.336, P.356, M.357, S.368, Q.369, G.371, F.372, Y.375 Ligands: ZN.1, MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.159, A:M.273, A:L.319, A:P.322, A:I.336, A:I.336, A:F.372, A:F.372 Hydrogen bonds: A:Y.159, A:Y.159, A:Q.369 Salt bridges: A:H.160, A:H.164 pi-Stacking: A:F.340, A:F.340, A:F.372, A:F.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y.Y. et al., Mangostanin Derivatives as Novel and Orally Active Phosphodiesterase 4 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem. (2021)

Release Date

2021-10-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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