SMTL ID : 8ylc.1

The crystal structure of PDE4D with Amentoflavone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.160, H.164, H.200, D.201, D.318 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.164, A:H.200, A:D.201, A:D.318, H2O.1, H2O.1 ZN.4: 5 residues within 4Å: Chain B: H.164, H.200, D.201, D.318 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.200, B:D.201, B:D.318, H2O.5, H2O.5

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.200, D.201, E.230 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.201, H2O.1, H2O.1, H2O.1, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain B: H.200, D.201 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.201, H2O.4, H2O.5, H2O.5, H2O.5, H2O.5

2 x 01: 8-[5-[5,7-bis(oxidanyl)-4-oxidanylidene-chromen-2-yl]-2-oxidanyl-phenyl]-2-(4-hydroxyphenyl)-5,7-bis(oxidanyl)chromen-4-one

01.3: 12 residues within 4Å: Chain A: Y.159, M.273, L.319, N.321, I.336, F.340, M.357, S.368, Q.369, G.371, F.372, I.376 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.372, A:F.372, A:I.376 Hydrogen bonds: A:N.321, A:Q.369 Water bridges: A:Y.159, A:H.160, A:D.318, A:D.318, A:Q.369 pi-Stacking: A:F.340, A:F.372, A:F.372 01.6: 9 residues within 4Å: Chain B: M.273, I.336, M.357, S.368, Q.369, G.371, F.372, Y.375, I.376 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.372, B:Y.375, B:I.376 Hydrogen bonds: B:Q.369 Water bridges: B:Q.369 pi-Stacking: B:F.372, B:F.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Discovery of amentoflavone as a natural PDE4 inhibitor with anti-fibrotic effects. Chin.Chem.Lett. (2024)

Release Date

2024-06-12

Peptides

3',5'-cyclic-AMP phosphodiesterase 4D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3',5'-cyclic-AMP phosphodiesterase 4D