SMTL ID : 7yqf.1

Crystal structure of PDE4D complexed with glycyrrhisoflavone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.6: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.7 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.6, H2O.8

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.137, E.166 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.1, H2O.1, H2O.2, H2O.3, H2O.4 MG.7: 3 residues within 4Å: Chain B: D.137, E.166 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.6, H2O.7, H2O.7, H2O.8, H2O.9

2 x JN0: 3-[3-(3-methylbut-2-enyl)-4,5-bis(oxidanyl)phenyl]-5,7-bis(oxidanyl)chromen-4-one(Non-covalent)

JN0.3: 12 residues within 4Å: Chain A: Y.95, M.209, N.257, Y.265, W.268, T.269, I.272, F.276, M.293, Q.305, F.308 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:N.257, A:F.276, A:F.308, A:F.308, A:F.308 Hydrogen bonds: A:N.257, A:Q.305 JN0.8: 14 residues within 4Å: Chain B: Y.95, M.209, N.257, Y.265, W.268, T.269, I.272, M.273, F.276, P.292, M.293, Q.305, F.308 Ligands: EDO.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.257, B:P.292, B:F.308, B:F.308, B:F.308 Hydrogen bonds: B:N.257, B:T.269, B:Q.305

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

EDO.4: 6 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 Ligands: JN0.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:P.292 Water bridges: A:Q.279 EDO.5: 5 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160, S.162 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:D.161, B:S.162, A:D.202 Hydrogen bonds: A:D.202 EDO.9: 6 residues within 4Å: Chain B: S.144, F.276, S.291, P.292, C.294 Ligands: JN0.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.144, B:S.144, B:P.292 Water bridges: B:S.291 EDO.10: 2 residues within 4Å: Chain B: R.266, W.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.266 EDO.11: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.161, A:S.162 Hydrogen bonds: B:D.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, H. et al., Bioactive compounds from Huashi Baidu decoction possess both antiviral and anti-inflammatory effects against COVID-19. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-07-12

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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