SMTL ID : 8wdn.1

Crystal structure of PDE4D complexed with 7b-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION

MG.1: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.2, H2O.2, H2O.2, H2O.5 MG.6: 3 residues within 4Å: Chain B: D.137, E.166 Ligands: ZN.7 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.5, H2O.5, H2O.6, H2O.7, H2O.7

2 x ZN: ZINC ION

ZN.2: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.1 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.136, A:D.137, A:D.254, H2O.1, H2O.3 ZN.7: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.100, B:H.136, B:D.137, B:D.254, H2O.5, H2O.5

2 x W8E: 3-[(2~{S},3~{R})-7-ethoxy-2-(3-ethoxy-4-methoxy-phenyl)-3-(hydroxymethyl)-2,3-dihydro-1-benzofuran-5-yl]propan-1-ol

W8E.3: 15 residues within 4Å: Chain A: Y.95, H.96, M.209, N.257, W.268, T.269, I.272, F.276, S.291, P.292, M.293, C.294, S.304, Q.305, F.308 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.276, A:F.308, A:F.308, A:F.308 Hydrogen bonds: A:H.96, A:P.292, A:Q.305 W8E.8: 14 residues within 4Å: Chain B: Y.95, H.96, N.257, W.268, T.269, I.272, F.276, S.291, P.292, M.293, C.294, S.304, Q.305, F.308 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.276, B:F.276, B:F.308, B:F.308 Hydrogen bonds: B:P.292, B:Q.305 Water bridges: B:H.96, B:H.96, B:D.254, B:Q.279

4 x EDO: 1,2-ETHANEDIOL

EDO.4: 5 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160, S.162 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.198, A:D.202 Water bridges: A:D.202, B:D.161, B:S.162 EDO.5: 4 residues within 4Å: Chain A: N.51, A.91, N.98, I.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.51, A:A.91, A:N.98 EDO.9: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.202 EDO.10: 4 residues within 4Å: Chain B: R.266, E.302, W.341, Y.342 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.266, B:E.302 Water bridges: B:Y.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gu, C. et al., Identification of Dihydrobenzofuran Neolignans as Novel PDE4 Inhibitors and Evaluation of Antiatopic Dermatitis Efficacy in DNCB-Induced Mice Model. J.Med.Chem. (2024)

Release Date

2024-08-28

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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