SMTL ID : 8k4c.1

Crystal structure of PDE4D complexed with ethaverine hydrochloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x VIC: 1-[(3,4-diethoxyphenyl)methyl]-6,7-diethoxy-isoquinoline(Non-covalent)

VIC.1: 9 residues within 4Å: Chain A: M.209, Y.265, T.269, I.272, F.276, M.293, Q.305, F.308, I.312 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.209, A:Y.265, A:I.272 Hydrogen bonds: A:Q.305 pi-Stacking: A:F.308 VIC.5: 12 residues within 4Å: Chain B: Y.95, M.209, N.257, Y.265, T.269, I.272, F.276, M.293, S.304, Q.305, F.308, I.312 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:M.209, B:N.257, B:Y.265, B:I.272, B:F.308 Hydrogen bonds: B:Q.305 pi-Stacking: B:F.308

2 x MG: MAGNESIUM ION(Non-covalent)

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

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.2 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.4, H2O.5

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: D.337, N.338, W.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.338

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors. Eur.J.Med.Chem. (2023)

Release Date

2023-11-22

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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